Contacts of the helix formed by residues 12 - 38 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ARG* 1.3 58.0 + - - +
14C ALA 3.6 0.9 - - - -
15C VAL* 3.9 27.7 - - - +
16C SER* 2.4 45.4 + - - -
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C SER* 1.3 71.8 - - - +
14C ALA* 1.3 63.5 + - - +
16C SER* 4.0 3.9 - - - -
17C ALA* 3.3 22.9 + - - +
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Residues in contact with ALA 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ARG* 1.3 77.3 - - - +
15C VAL* 1.3 61.9 + - + +
17C ALA* 3.3 4.9 + - - +
18C LYS* 3.0 35.4 + - + +
57C TYR* 5.0 0.2 - - - -
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Residues in contact with VAL 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C SER* 3.7 24.6 + - - +
13C ARG 3.4 0.4 - - - -
14C ALA* 1.3 77.2 - - + +
16C SER* 1.3 66.5 + - - +
18C LYS 3.5 0.2 + - - -
19C LYS* 3.0 27.4 + - + +
57C TYR* 3.6 32.6 - - + +
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Residues in contact with SER 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C SER 2.4 33.0 + - - -
13C ARG* 4.0 4.7 - - - -
15C VAL* 1.3 78.5 - - - +
17C ALA* 1.3 57.7 + - - +
19C LYS* 3.3 9.0 + - - +
20C LYS* 2.9 31.7 + - - +
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Residues in contact with ALA 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ARG 3.3 16.1 + - - +
14C ALA* 3.3 6.0 + - - +
15C VAL 3.2 0.4 - - - -
16C SER* 1.3 76.7 - - - +
18C LYS* 1.3 61.0 + - - +
20C LYS* 3.3 12.2 + - + +
21C ALA* 2.9 29.0 + - - +
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Residues in contact with LYS 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA* 3.0 19.8 + - - +
15C VAL 3.9 0.2 - - - +
17C ALA* 1.3 74.5 - - - +
19C LYS* 1.3 65.8 + - - +
21C ALA* 3.1 7.9 + - + +
22C ILE* 2.8 31.8 + - + +
48C GLY 5.5 1.1 - - - -
49C VAL* 4.1 23.1 - - + -
53C ASN* 2.8 30.1 + - - +
57C TYR* 3.8 27.2 + - + +
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Residues in contact with LYS 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL* 3.0 16.0 + - + +
16C SER* 3.3 13.2 - - - +
18C LYS* 1.3 79.3 - - - +
20C LYS* 1.3 63.4 + - - +
22C ILE* 3.2 5.6 + - - +
23C LEU* 3.0 36.8 + - + +
57C TYR* 4.2 27.6 + - + -
58C PHE* 3.4 31.2 - - + -
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Residues in contact with LYS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C SER* 2.9 15.4 + - - +
17C ALA* 3.4 14.4 - - + +
19C LYS* 1.3 75.7 - - - +
21C ALA* 1.3 61.8 + - - +
23C LEU* 3.4 7.4 + - - +
24C SER* 3.0 26.6 + - - -
71C GLN* 6.3 0.7 - - - +
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ALA 2.9 17.3 + - - +
18C LYS* 3.1 7.6 + - + +
20C LYS* 1.3 75.9 - - - +
22C ILE* 1.3 63.1 + - + +
24C SER* 3.9 4.5 - - - -
25C ALA* 2.9 26.7 + - - +
47C ALA* 3.7 26.2 - - + +
49C VAL* 6.0 0.7 - - + -
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LYS* 2.8 22.1 + - + +
19C LYS 3.6 4.3 - - - +
21C ALA* 1.3 76.2 - - - +
23C LEU* 1.3 50.7 + - - +
25C ALA* 3.3 1.6 + - - +
26C ALA* 2.7 36.4 + - - +
43C ILE* 3.8 1.5 - - + +
47C ALA* 3.9 18.6 - - + -
49C VAL* 4.2 19.7 - - + -
54C LEU* 4.0 34.3 - - + +
57C TYR* 3.9 34.3 - - + -
58C PHE* 3.7 26.0 - - + -
64C LEU* 4.1 10.5 - - + -
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LYS* 3.0 35.7 + - + +
20C LYS* 3.9 6.3 - - + +
21C ALA 3.4 0.2 - - - -
22C ILE* 1.3 75.9 - - - +
24C SER* 1.3 57.2 + - - +
26C ALA* 3.1 5.1 + - - +
27C LEU* 2.9 30.4 + - - +
58C PHE* 3.7 29.4 - - + -
64C LEU* 3.8 13.5 - - + -
67C ALA* 4.0 18.4 - - + +
68C VAL* 4.1 18.8 - - + +
71C GLN* 3.7 34.8 - - + +
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Residues in contact with SER 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LYS 3.0 17.3 + - - -
21C ALA* 3.9 5.2 - - - -
23C LEU* 1.3 76.8 - - - +
25C ALA* 1.3 57.6 + - - +
27C LEU* 3.3 9.5 + - - +
28C ASP* 3.1 38.4 + - - +
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA 2.9 18.1 + - - +
22C ILE 3.7 2.7 - - - +
24C SER* 1.3 73.8 + - - +
26C ALA* 1.3 64.6 + - - +
28C ASP* 3.9 1.0 - - - +
29C THR* 2.6 33.6 + - - -
43C ILE* 3.7 25.4 - - + +
46C LEU* 3.8 20.6 - - + -
47C ALA* 3.8 15.5 - - + +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE 2.7 22.0 + - - +
23C LEU 3.1 5.1 + - - +
25C ALA* 1.3 73.4 - - - +
27C LEU* 1.3 55.1 + - - +
29C THR 3.2 0.3 + - - -
30C PHE* 2.7 45.6 + - + -
43C ILE* 3.7 13.6 - - + +
64C LEU* 3.7 36.8 - - + -
68C VAL* 3.8 9.6 - - + -
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU 2.9 16.3 + - - +
24C SER* 3.6 9.4 - - - +
25C ALA 3.2 0.2 - - - -
26C ALA* 1.3 76.3 - - - +
28C ASP* 1.3 54.5 + - - +
30C PHE* 4.4 0.2 - - - +
31C SER* 2.6 37.0 + - - +
68C VAL* 4.2 17.4 - - + +
107C TYR* 6.3 0.7 - - + -
109C GLN* 3.6 56.1 - - + +
110C ALA* 3.9 16.8 - - + +
113C LEU* 3.6 24.0 - - + -
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Residues in contact with ASP 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C SER* 3.1 23.6 + - - +
25C ALA* 3.9 3.3 - - - +
27C LEU* 1.3 83.7 - - - +
29C THR* 1.3 62.3 + - - +
31C SER* 3.5 5.2 + - - -
32C GLN* 3.2 22.7 + - - +
46C LEU* 4.0 19.1 - - + +
109C GLN* 4.7 9.6 - - - +
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Residues in contact with THR 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ALA 2.6 23.1 + - - -
28C ASP* 1.3 75.6 - - - +
30C PHE* 1.3 65.5 + - - +
32C GLN* 3.1 4.4 + - - -
33C PHE* 2.9 28.5 + - + -
38C THR* 3.2 29.2 + - + -
42C GLN* 3.5 28.6 + - + +
43C ILE* 3.7 21.3 + - + +
46C LEU* 3.7 13.9 - - - +
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Residues in contact with PHE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ALA* 2.7 46.4 + - + +
29C THR* 1.3 72.7 - - - +
31C SER* 1.3 56.2 + - - +
34C GLY* 2.5 34.2 + - - -
35C PHE* 3.9 14.6 - + - -
38C THR* 3.5 31.2 - - + -
43C ILE* 4.1 8.7 - - + -
61C LYS* 4.0 26.2 - - + -
64C LEU* 4.1 3.8 - - + -
65C TYR* 3.6 53.8 - + + -
68C VAL* 4.2 7.4 - - + -
113C LEU* 3.8 24.3 - - + +
116C MSE 4.7 1.0 - - - +
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Residues in contact with SER 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 2.6 28.2 + - - +
28C ASP* 3.5 8.0 + - - -
30C PHE* 1.3 79.5 - - - +
32C GLN* 1.3 62.9 + - - +
34C GLY 4.5 0.5 + - - -
109C GLN* 4.8 12.7 - - - +
112C ARG* 5.5 1.3 - - - -
113C LEU* 3.8 16.9 - - - +
116C MSE 4.0 31.7 - - - +
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Residues in contact with GLN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ASP 3.2 17.1 + - - +
29C THR* 3.1 2.3 + - - -
31C SER* 1.3 81.2 - - - +
33C PHE* 1.3 84.5 + - + +
34C GLY 3.8 0.2 + - - -
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Residues in contact with PHE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C THR* 2.9 18.8 + - + -
32C GLN* 1.3 89.2 - - + +
34C GLY* 1.3 63.4 + - - +
37C GLY* 3.3 22.3 + - - -
38C THR* 3.6 21.3 - - - +
42C GLN* 3.5 32.5 - - - -
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Residues in contact with GLY 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 2.5 28.7 + - - -
31C SER 4.4 0.8 + - - -
32C GLN 3.6 2.0 + - - -
33C PHE* 1.3 75.9 - - - +
35C PHE* 1.3 64.2 + - - -
36C HIS 3.3 1.3 - - - -
38C THR* 2.6 27.1 + - - -
113C LEU* 5.8 1.3 - - - -
116C MSE 5.6 5.8 - - - -
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 3.9 12.6 - + - -
34C GLY* 1.3 74.1 - - - +
36C HIS* 1.3 92.0 - + + +
38C THR* 3.6 5.9 + - - +
61C LYS* 3.0 54.6 + - + +
62C GLU* 3.7 36.8 - - + -
65C TYR* 3.7 39.4 + + + +
117C GLU* 5.8 0.2 - - - +
124C LEU* 3.6 30.1 - - + -
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Residues in contact with HIS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 1.3 108.9 - + + +
37C GLY* 1.3 65.4 + - - +
38C THR 3.3 1.7 + - - +
39C ARG* 5.8 0.3 - - - +
61C LYS* 3.3 18.1 + - - +
123C PRO* 6.1 2.8 - - - +
124C LEU* 5.2 3.8 - - + +
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Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 3.3 29.7 + - - +
34C GLY 4.1 0.2 - - - -
36C HIS* 1.3 80.0 - - - +
38C THR* 1.3 59.6 + - - +
39C ARG* 3.6 9.7 + - - +
42C GLN* 4.4 4.7 - - - +
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Residues in contact with THR 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C THR* 3.2 41.4 + - + -
30C PHE* 3.5 19.0 - - + -
33C PHE* 3.6 8.6 - - - +
34C GLY 2.6 24.5 + - - -
35C PHE 3.8 2.7 - - - -
36C HIS 3.2 3.1 - - - +
37C GLY* 1.3 76.0 - - - +
39C ARG* 1.3 73.2 + - - +
42C GLN* 4.2 2.5 - - - +
43C ILE* 3.7 17.5 - - + -
61C LYS* 3.1 27.1 + - + +
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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