Contacts of the helix formed by residues 12 - 38 (chain A) in PDB entry 3LOC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 12 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ARG* 1.3 77.3 + - - +
13A ARG* 1.3 64.9 + - - +
14A ALA 3.6 1.3 - - - -
15A VAL* 3.4 24.9 + - - +
16A SER* 3.1 26.1 + - - -
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ARG 4.3 0.4 - - - -
12A SER* 1.3 71.1 - - - +
14A ALA* 1.3 63.6 + - + +
16A SER* 3.9 4.7 - - - -
17A ALA* 3.4 21.0 + - - +
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER 3.6 0.2 - - - -
13A ARG* 1.3 76.7 - - + +
15A VAL* 1.3 61.9 + - + +
17A ALA* 3.5 6.8 + - - +
18A LYS* 3.0 41.7 + - - +
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 3.6 27.1 - - - +
13A ARG 3.3 0.4 - - - -
14A ALA* 1.3 75.5 - - + +
16A SER* 1.3 69.2 + - - +
18A LYS 3.1 2.4 + - - -
19A LYS* 3.0 28.4 + - + +
57A TYR* 3.4 30.1 + - + +
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Residues in contact with SER 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER 3.1 16.0 + - - -
13A ARG* 3.9 5.6 - - - -
15A VAL* 1.3 80.5 - - - +
17A ALA* 1.3 57.8 + - - +
19A LYS* 3.3 8.0 + - - +
20A LYS* 3.0 36.0 + - - +
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG 3.4 15.2 + - - +
14A ALA* 3.8 7.6 - - - +
15A VAL 3.1 0.4 - - - -
16A SER* 1.3 80.2 + - - +
18A LYS* 1.3 57.0 + - + +
20A LYS* 3.4 6.2 + - - +
21A ALA* 2.9 28.7 + - - +
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA* 3.0 25.4 + - + +
17A ALA* 1.3 72.4 - - - +
19A LYS* 1.3 69.1 + - - +
21A ALA* 3.1 7.2 + - - +
22A ILE* 2.8 29.7 + - + +
48A GLY 5.6 1.3 - - - -
49A VAL* 4.2 20.4 - - + +
53A ASN* 2.5 33.3 + - - +
57A TYR* 3.3 33.4 - - + +
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Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.0 15.3 + - + +
16A SER* 3.6 11.7 - - - +
18A LYS* 1.3 77.0 - - - +
20A LYS* 1.3 59.7 + - + +
22A ILE* 3.1 5.9 + - - +
23A LEU* 2.9 42.5 + - + +
57A TYR* 3.7 33.3 + - + -
58A PHE* 3.8 31.3 - - + -
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Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER* 3.0 24.9 + - - +
17A ALA* 3.9 5.8 - - - +
19A LYS* 1.3 78.1 - - + +
21A ALA* 1.3 60.8 + - - +
23A LEU* 3.4 10.7 + - + +
24A SER* 3.0 27.8 + - - -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 2.9 17.0 + - - +
18A LYS* 3.1 8.3 + - - +
20A LYS* 1.3 78.8 - - - +
22A ILE* 1.3 57.3 + - + +
24A SER* 3.9 4.0 - - - -
25A ALA* 2.9 31.0 + - - +
47A ALA* 3.6 26.2 - - + +
49A VAL* 5.6 0.7 - - + -
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS 2.8 25.1 + - - +
19A LYS 3.6 3.6 - - - +
21A ALA* 1.3 74.1 - - - +
23A LEU* 1.3 53.3 + - - +
25A ALA* 3.2 2.2 + - - +
26A ALA* 2.6 37.2 + - - +
43A ILE* 3.9 1.6 - - + +
47A ALA* 4.0 9.4 - - + -
49A VAL* 4.2 25.4 - - + -
53A ASN 5.1 0.2 - - - -
54A LEU* 3.9 27.1 - - + -
57A TYR* 3.7 37.0 - - + -
58A PHE* 3.6 24.9 - - + -
64A LEU* 3.9 18.6 - - + -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 2.9 33.5 + - + +
20A LYS* 3.4 10.3 + - + +
22A ILE* 1.3 75.2 - - - +
24A SER* 1.3 58.9 + - - +
26A ALA* 3.3 4.5 + - - +
27A LEU* 2.8 29.1 + - - +
58A PHE* 3.8 26.0 - - + -
64A LEU* 4.1 11.4 - - + -
67A ALA* 4.1 16.2 - - + -
68A VAL* 4.2 11.1 - - + +
71A GLN* 3.5 40.3 + - - +
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Residues in contact with SER 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS 3.0 17.9 + - - -
21A ALA* 3.9 4.3 - - - -
23A LEU* 1.3 75.5 - - - +
25A ALA* 1.3 65.5 + - - +
27A LEU* 3.2 8.7 + - - +
28A ASP* 3.0 32.7 + - - +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA 2.9 20.4 + - - +
22A ILE 3.6 3.6 - - - +
24A SER* 1.3 77.5 + - - +
26A ALA* 1.3 62.9 + - - +
28A ASP* 3.8 1.3 - - - +
29A THR* 3.0 30.8 + - - -
43A ILE* 3.5 28.7 - - + +
46A LEU* 4.0 20.4 - - + -
47A ALA* 3.7 12.6 - - + +
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE 2.6 21.9 + - - +
23A LEU 3.5 4.7 - - - +
25A ALA* 1.3 70.9 - - - +
27A LEU* 1.3 65.9 + - - +
29A THR 3.2 0.9 + - - -
30A PHE* 2.9 35.6 + - + -
43A ILE* 3.7 11.6 - - - +
64A LEU* 3.7 28.3 - - + -
68A VAL* 3.7 17.9 - - + -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 2.8 19.8 + - - +
24A SER* 3.2 8.7 + - - +
26A ALA* 1.3 74.4 - - - +
28A ASP* 1.3 56.3 + - - +
30A PHE* 4.0 1.2 - - - +
31A SER* 2.6 31.3 + - - +
68A VAL* 4.3 17.0 - - + +
71A GLN* 6.3 0.9 - - - +
109A GLN* 3.8 43.5 - - + +
110A ALA* 3.9 27.1 - - + +
113A LEU* 4.1 19.7 - - + -
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Residues in contact with ASP 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A SER* 3.0 22.3 + - - +
25A ALA* 3.8 3.5 - - - +
27A LEU* 1.3 80.0 - - - +
29A THR* 1.3 61.4 + - - +
31A SER* 3.4 6.1 + - - -
32A GLN* 3.3 24.1 + - - +
46A LEU* 4.3 17.3 - - + +
109A GLN* 2.6 41.0 + - - +
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA 3.0 19.4 + - - -
28A ASP* 1.3 72.9 - - - +
30A PHE* 1.3 68.4 + - - +
32A GLN* 3.2 4.7 + - - -
33A PHE* 3.0 25.2 + - + -
38A THR* 3.5 30.3 + - + +
42A GLN* 3.5 28.7 + - + +
43A ILE* 4.0 17.1 + - + +
46A LEU* 3.4 18.4 - - - +
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Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 2.9 34.5 + - + +
29A THR* 1.3 77.9 - - - +
31A SER* 1.3 57.3 + - - +
34A GLY* 2.6 38.9 + - - -
35A PHE* 3.9 16.6 - + - -
38A THR* 3.4 28.9 - - + -
43A ILE* 3.9 20.2 - - + -
61A LYS* 4.0 17.5 - - + -
64A LEU* 4.4 2.9 - - + -
65A TYR* 3.7 53.8 - + + -
68A VAL* 4.6 4.9 - - + -
113A LEU* 3.7 23.4 - - + +
116A MSE 4.7 1.0 - - - +
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU 2.6 23.5 + - - -
28A ASP 3.4 4.0 + - - -
30A PHE* 1.3 76.9 - - - +
32A GLN* 1.3 61.5 + - - +
109A GLN* 3.3 30.6 + - - +
112A ARG* 5.8 1.8 - - - -
113A LEU* 3.5 24.5 - - - -
116A MSE 3.1 35.4 - - - +
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Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASP 3.3 19.2 + - - +
29A THR* 3.2 7.7 + - - +
31A SER* 1.3 81.9 - - - +
33A PHE* 1.3 91.7 + - + +
34A GLY 3.7 0.9 - - - -
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR* 3.0 20.8 + - + +
32A GLN* 1.3 106.1 - - + +
34A GLY* 1.3 63.7 + - - +
37A GLY* 3.1 36.1 + - - -
38A THR* 3.8 2.7 - - - +
42A GLN* 3.3 30.5 - - - -
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 2.6 27.1 + - - -
31A SER 4.7 0.2 - - - -
32A GLN 3.7 1.4 - - - -
33A PHE* 1.3 75.0 - - - +
35A PHE* 1.3 61.9 + - - -
36A HIS 3.4 1.1 - - - -
37A GLY 4.6 0.2 - - - -
38A THR* 2.6 29.6 + - - -
65A TYR* 6.1 0.2 - - - -
113A LEU* 5.9 0.9 - - - -
116A MSE 5.8 4.4 - - - -
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 3.9 12.2 - + - -
34A GLY* 1.3 73.2 - - - +
36A HIS* 1.3 94.6 + + + +
38A THR* 3.6 6.8 + - - +
61A LYS* 3.0 65.4 + - + +
62A GLU* 3.8 20.9 - - + -
65A TYR* 3.7 30.9 + + + +
117A GLU* 5.6 0.2 - - - +
124A LEU* 3.3 40.6 - - + -
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Residues in contact with HIS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY 3.4 0.2 - - - -
35A PHE* 1.3 105.6 - + + +
37A GLY* 1.3 63.8 + - - +
38A THR 3.3 4.2 + - - +
39A ARG* 5.9 0.3 - - - +
61A LYS* 3.9 8.2 + - - +
123A PRO* 6.1 2.8 - - - +
124A LEU* 5.5 2.4 - - + +
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Residues in contact with GLY 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.1 31.4 + - - +
34A GLY* 4.6 0.2 - - - -
36A HIS* 1.3 78.7 - - - +
38A THR* 1.3 62.2 + - - +
39A ARG* 4.6 5.4 + - - +
42A GLN* 3.7 9.2 - - - +
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Residues in contact with THR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 3.5 35.2 + - + +
30A PHE* 3.4 17.5 - - + -
33A PHE* 3.8 3.1 - - - +
34A GLY 2.6 22.8 + - - -
35A PHE 3.7 6.3 - - - -
36A HIS 3.3 1.6 - - - +
37A GLY* 1.3 78.6 - - - +
39A ARG* 1.3 78.4 + - - +
42A GLN* 3.8 4.9 - - - -
43A ILE* 3.7 19.1 - - + -
61A LYS* 2.8 32.2 + - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il