Contacts of the helix formed by residues 12 - 34 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ARG* 1.3 73.5 - - - +
13D ARG* 1.3 64.5 + - - +
14D ALA* 3.5 7.8 + - - +
15D VAL* 3.1 37.4 + - - +
16D SER* 3.0 24.4 + - - -
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Residues in contact with ARG 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ARG 5.2 5.4 - - - +
12D SER* 1.3 72.3 + - - +
14D ALA* 1.3 53.4 + - - +
16D SER* 3.0 8.2 + - - +
17D ALA* 2.8 37.0 + - - +
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Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D SER* 3.4 7.3 + - - +
13D ARG* 1.3 78.0 - - - +
15D VAL* 1.3 63.6 + - + +
17D ALA* 3.4 6.4 + - - +
18D LYS* 3.1 22.3 + - - +
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Residues in contact with VAL 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D SER* 3.1 29.9 + - - +
14D ALA* 1.3 74.3 - - + +
16D SER* 1.3 66.1 + - - +
18D LYS* 3.2 5.3 + - - +
19D LYS* 2.9 32.3 + - + +
57D TYR* 3.7 38.0 + - + +
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Residues in contact with SER 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D SER 3.0 16.4 + - - -
13D ARG* 3.0 13.9 + - - +
15D VAL* 1.3 78.0 - - - +
17D ALA* 1.3 64.7 + - - +
19D LYS* 3.2 13.8 + - - +
20D LYS* 2.9 44.5 + - - +
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Residues in contact with ALA 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ARG 2.8 23.0 + - - +
14D ALA* 3.7 7.0 - - - +
16D SER* 1.3 72.8 + - - +
18D LYS* 1.3 58.0 + - - +
20D LYS* 3.2 9.9 + - - +
21D ALA* 3.0 27.5 + - - +
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Residues in contact with LYS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ALA 3.1 14.6 + - - +
15D VAL* 3.2 8.5 + - - +
17D ALA* 1.3 76.1 - - - +
19D LYS* 1.3 61.5 + - - +
21D ALA* 3.2 7.4 + - + +
22D ILE* 3.1 35.3 + - + +
48D GLY 4.7 2.8 + - - -
49D VAL* 3.3 30.2 - - + +
53D ASN* 3.0 31.0 + - - +
57D TYR* 4.6 12.3 - - + +
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Residues in contact with LYS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D VAL* 2.9 33.4 + - + +
16D SER* 3.6 10.3 - - - +
18D LYS* 1.3 76.1 - - - +
20D LYS* 1.3 59.3 + - + +
22D ILE* 3.2 8.6 + - - +
23D LEU* 2.9 40.1 + - + +
57D TYR* 3.7 37.3 + - + +
58D PHE* 4.4 21.6 - - + -
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Residues in contact with LYS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D SER* 2.9 34.7 + - - +
17D ALA* 3.7 7.9 - - - +
19D LYS* 1.3 74.5 - - + +
21D ALA* 1.3 60.6 + - - +
23D LEU* 4.0 8.0 - - + +
24D SER* 2.8 33.7 + - - -
71D GLN* 5.0 11.9 - - - +
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ALA 3.0 13.9 + - - +
18D LYS* 3.2 13.0 + - + +
20D LYS* 1.3 77.0 - - - +
22D ILE* 1.3 57.5 + - + +
24D SER* 3.8 4.3 - - - -
25D ALA* 3.0 28.8 + - - +
47D ALA* 4.0 18.9 - - + +
49D VAL* 5.9 1.8 - - + -
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Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LYS* 3.1 28.9 + - + +
19D LYS* 3.7 5.2 - - - +
21D ALA* 1.3 73.3 - - - +
23D LEU* 1.3 56.4 + - - +
25D ALA* 3.2 3.5 + - - +
26D ALA* 2.7 36.7 + - - +
43D ILE* 3.9 3.2 - - + +
47D ALA* 4.2 6.7 - - + -
49D VAL* 4.3 20.4 - - + -
53D ASN* 5.1 0.4 - - - +
54D LEU* 4.0 35.7 - - + +
57D TYR* 4.1 26.7 - - + -
58D PHE* 3.7 27.6 - - + -
64D LEU* 4.1 9.2 - - + -
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LYS* 2.9 30.0 + - + +
20D LYS* 4.0 5.6 - - + +
22D ILE* 1.3 75.2 - - - +
24D SER* 1.3 58.2 + - - +
26D ALA* 3.2 5.0 + - - +
27D LEU* 2.9 29.9 + - - +
58D PHE* 3.8 14.1 - - + -
64D LEU* 3.7 15.3 - - + -
67D ALA* 3.7 32.8 - - + +
68D VAL* 3.8 18.6 - - + +
71D GLN* 3.5 39.7 - - + +
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Residues in contact with SER 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LYS 2.8 23.7 + - - -
21D ALA* 3.8 5.2 - - - -
23D LEU* 1.3 73.5 - - - +
25D ALA* 1.3 62.1 + - - +
26D ALA 3.2 0.2 + - - -
27D LEU* 3.2 8.3 + - - +
28D ASP* 3.2 31.5 + - - -
71D GLN* 5.6 0.6 - - - +
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ALA 3.0 18.9 + - - +
22D ILE 3.5 3.6 - - - +
24D SER* 1.3 75.5 + - - +
26D ALA* 1.3 55.8 + - - +
28D ASP* 3.5 1.2 + - - -
29D THR* 2.8 37.1 + - - -
43D ILE* 3.8 14.4 - - + +
46D LEU* 3.6 19.8 - - + +
47D ALA* 3.6 28.7 - - + +
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE 2.7 21.3 + - - +
23D LEU 3.5 4.5 - - - +
25D ALA* 1.3 70.9 - - - +
27D LEU* 1.3 60.7 + - - +
29D THR* 3.9 0.2 - - - -
30D PHE* 2.7 39.3 + - + -
43D ILE* 3.7 16.1 - - + +
64D LEU* 3.7 28.3 - - + -
68D VAL* 3.6 17.7 - - + -
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU 2.9 14.3 + - - +
24D SER* 3.7 10.3 - - - +
26D ALA* 1.3 75.6 - - - +
28D ASP* 1.3 68.5 + - - +
30D PHE* 3.8 1.3 - - - -
31D SER* 2.8 28.1 + - - +
68D VAL* 4.1 20.5 - - + +
71D GLN* 5.6 5.6 - - - +
72D ILE* 5.8 0.9 - - + -
107D TYR* 6.0 4.9 - - + -
109D GLN* 3.9 23.3 - - + +
110D ALA* 3.9 39.3 - - + +
113D LEU* 4.1 16.4 - - + -
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Residues in contact with ASP 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D SER* 3.2 17.9 + - - +
25D ALA* 3.7 7.8 - - - +
27D LEU* 1.3 84.9 - - - +
29D THR* 1.3 63.6 + - - +
31D SER* 3.2 13.0 + - - -
32D GLN* 3.3 18.2 + - - +
46D LEU* 4.0 17.4 - - + +
109D GLN* 3.3 28.8 + - - +
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Residues in contact with THR 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ALA 2.8 19.3 + - - -
28D ASP* 1.3 73.3 - - - +
30D PHE* 1.3 67.0 + - - +
32D GLN* 3.0 11.2 + - - -
33D PHE* 3.0 32.5 + - + -
38D THR* 3.5 26.5 + - + +
42D GLN* 4.0 21.6 + - + +
43D ILE* 3.9 15.8 - - + +
46D LEU* 3.6 14.9 - - - +
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Residues in contact with PHE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ALA* 2.7 38.3 + - + +
27D LEU 4.0 2.0 - - - +
29D THR* 1.3 72.5 - - - +
31D SER* 1.3 58.0 + - - +
34D GLY* 2.7 38.8 + - - -
35D PHE* 4.0 11.4 - + - -
38D THR* 3.7 30.5 - - + -
43D ILE* 3.9 21.1 - - + -
61D LYS* 3.9 27.6 - - + -
64D LEU* 4.3 2.7 - - + -
65D TYR* 3.6 49.1 - + + -
68D VAL* 4.4 6.3 - - + -
113D LEU* 3.9 22.6 - - + +
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Residues in contact with SER 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 2.8 23.4 + - - -
28D ASP 3.2 7.1 + - - -
30D PHE* 1.3 77.1 - - - +
32D GLN* 1.3 68.9 + - - +
34D GLY 4.6 0.2 - - - -
109D GLN* 3.4 41.5 + - - +
112D ARG* 5.2 10.2 + - - -
113D LEU* 3.9 16.0 - - - +
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Residues in contact with GLN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ASP 3.3 16.9 + - - +
29D THR* 3.0 5.1 + - - +
31D SER* 1.3 88.7 - - - +
33D PHE* 1.3 80.9 + - + +
109D GLN* 5.2 4.9 - - - +
112D ARG* 5.2 7.3 + - - -
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Residues in contact with PHE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D THR* 3.0 24.3 + - + -
32D GLN* 1.3 92.8 - - + +
34D GLY* 1.3 63.7 + - - +
37D GLY* 3.4 27.1 + - - +
38D THR* 3.7 11.4 - - - +
42D GLN* 3.1 30.7 - - - -
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Residues in contact with GLY 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D PHE* 2.7 28.2 + - - -
31D SER 4.6 0.4 - - - -
32D GLN 3.8 0.8 - - - -
33D PHE* 1.3 71.4 - - - +
35D PHE* 1.3 65.9 + - - -
36D HIS 3.3 2.0 - - - -
37D GLY 3.8 0.4 - - - -
38D THR* 2.8 25.1 + - - -
113D LEU* 5.8 1.8 - - - -
116D MSE 6.4 2.2 - - - -
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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