Contacts of the helix formed by residues 30 - 45 (chain C) in PDB entry 6XAV
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 ARG 30 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LEU* 5.5 15.0 - - + +
29C MET* 1.3 77.8 - - - +
31C LYS* 1.3 61.5 + - - +
32C GLN* 3.3 51.3 + - - +
33C ASP* 3.3 27.5 + - - +
34C ILE* 3.0 28.3 + - - +
76C PRO* 5.3 5.6 - - - +
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Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU 4.3 6.3 - - - -
7C LYS* 3.4 25.2 + - - +
8C ASN* 4.3 3.2 + - - +
9C THR 3.1 27.2 + - - -
10C PRO* 5.1 1.4 - - - +
11C VAL* 4.5 24.0 - - + +
14C LEU* 3.7 21.1 - - + -
30C ARG* 1.3 74.4 - - - +
32C GLN* 1.3 66.0 + - + +
34C ILE* 3.2 10.3 + - - +
35C ILE* 3.1 30.8 + - + +
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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
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7C LYS* 5.2 14.7 - - - +
30C ARG* 3.3 36.7 + - - +
31C LYS* 1.3 79.6 - - + +
33C ASP* 1.3 60.7 + - - +
35C ILE* 3.6 7.1 + - + +
36C PHE* 3.0 23.7 + - - +
70C SER* 5.2 7.5 + - - -
75C GLY* 5.7 2.2 - - - -
76C PRO* 3.4 29.8 - - + +
77C ASP* 3.1 27.7 - - + +
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Residues in contact with ASP 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C MET* 3.8 23.1 - - + +
30C ARG* 3.3 42.4 + - - +
31C LYS 3.3 0.4 - - - -
32C GLN* 1.3 76.9 - - - +
34C ILE* 1.3 60.3 + - - +
36C PHE* 3.8 8.0 - - - +
37C ALA* 2.9 29.8 + - - +
76C PRO* 6.1 1.7 - - - +
77C ASP* 5.3 1.4 - - - +
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C VAL* 4.5 9.6 - - + -
14C LEU* 3.7 29.2 - - + +
15C ILE* 3.7 22.2 - - + +
26C LEU* 3.6 49.6 - - + +
29C MET* 4.0 15.9 - - + +
30C ARG 3.0 22.8 + - - +
31C LYS* 3.2 7.4 + - - +
33C ASP* 1.3 75.0 - - - +
35C ILE* 1.3 61.8 + - - +
37C ALA* 3.1 6.4 + - - +
38C ILE* 2.8 38.8 + - + +
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Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 5.1 6.3 - - + -
6C LEU* 3.3 55.2 - - + +
7C LYS* 4.1 18.2 - - + +
14C LEU* 3.8 23.8 - - + -
31C LYS* 3.1 26.5 + - + +
32C GLN* 4.1 6.3 - - + +
34C ILE* 1.3 75.3 - - - +
36C PHE* 1.3 57.8 + - - +
38C ILE* 3.3 6.4 + - - +
39C LEU* 2.9 41.1 + - + +
77C ASP* 5.6 0.9 - - - +
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Residues in contact with PHE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLN 3.0 19.7 + - - +
33C ASP* 3.8 8.7 - - - +
34C ILE 3.2 0.2 - - - -
35C ILE* 1.3 77.8 - - - +
37C ALA* 1.3 62.6 + - + +
39C LEU* 3.6 5.1 + - - +
40C LYS* 3.3 56.9 + - + +
76C PRO 6.1 0.2 - - - -
77C ASP* 3.6 22.4 + - - +
104C PRO* 3.6 33.4 - - + -
109C ARG* 5.5 5.8 - - - -
111C PHE* 3.5 29.2 - + - -
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 3.6 25.0 - - + +
26C LEU* 5.8 3.1 - - + -
29C MET* 4.8 9.9 - - + -
33C ASP 2.9 19.4 + - - +
34C ILE* 3.6 5.8 - - - +
36C PHE* 1.3 78.5 - - + +
38C ILE* 1.3 64.1 + - - +
40C LYS* 3.4 7.3 + - - +
41C GLN* 3.2 18.4 + - - +
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Residues in contact with ILE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 4.9 14.8 - - + -
6C LEU* 5.1 8.1 - - + -
14C LEU* 3.8 35.9 - - + +
17C LEU* 3.8 33.0 - - + -
18C GLY* 4.3 6.7 - - - +
21C MET* 5.6 3.8 - - + -
23C LEU* 4.2 14.8 - - + -
26C LEU* 5.0 0.9 - - + -
34C ILE* 2.8 31.3 + - + +
35C ILE* 3.3 6.0 + - - +
37C ALA* 1.3 74.6 - - - +
39C LEU* 1.3 61.7 + - + +
41C GLN* 3.3 2.5 + - - +
42C HIS* 2.8 31.3 + - + +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 4.0 18.6 - - + +
3C LEU* 4.0 26.5 - - + -
6C LEU* 3.8 21.3 - - + -
35C ILE* 2.9 30.3 + - + +
36C PHE* 4.0 4.0 - - - +
37C ALA 3.4 0.2 - - - -
38C ILE* 1.3 76.3 - - - +
40C LYS* 1.3 57.8 + - - +
42C HIS* 3.9 2.4 - - + -
43C ALA* 3.0 30.0 + - - +
49C ILE* 3.3 40.7 - - + +
101C ILE* 5.8 0.2 - - + -
103C PRO* 5.3 0.4 - - - -
111C PHE* 4.1 25.8 - - + -
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Residues in contact with LYS 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PHE* 3.3 52.2 + - + +
37C ALA* 3.8 7.2 - - - +
38C ILE 3.2 0.6 - - - -
39C LEU* 1.3 77.5 - - + +
41C GLN* 1.3 61.9 + - - +
43C ALA* 3.2 4.9 + - - +
44C LYS* 3.0 49.2 + - - +
103C PRO* 4.9 15.0 - - + -
104C PRO* 5.5 7.6 - - + +
111C PHE* 6.0 0.9 - - + -
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Residues in contact with GLN 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C MET* 3.9 36.5 + - + +
22C GLY 5.9 0.4 + - - -
23C LEU* 3.6 32.9 - - + +
37C ALA 3.2 14.2 + - - +
38C ILE* 3.9 3.1 - - - +
40C LYS* 1.3 79.0 - - - +
42C HIS* 1.3 62.8 + - - +
44C LYS* 3.5 32.0 + - - +
45C SER* 3.7 16.7 + - - -
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Residues in contact with HIS 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.4 48.8 - - + +
21C MET* 5.2 12.4 - - + +
38C ILE* 2.8 22.4 + - + +
39C LEU* 4.0 6.5 - - + +
41C GLN* 1.3 78.0 - - - +
43C ALA* 1.3 60.4 + - - +
45C SER* 3.6 11.8 + - - -
47C GLU* 3.4 59.2 + - + +
48C ASP 4.6 3.4 - - - -
49C ILE* 5.4 4.7 - - + -
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU 3.0 18.8 + - - +
40C LYS 3.2 3.6 + - - +
42C HIS* 1.3 74.5 - - - +
44C LYS* 1.3 64.3 + - + +
45C SER 3.1 2.2 - - - -
46C GLY* 3.1 14.6 + - - -
47C GLU 3.9 16.1 + - - +
49C ILE* 3.8 8.7 - - + +
103C PRO* 3.7 28.0 - - + -
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LYS* 3.0 42.6 + - - +
41C GLN* 3.8 28.3 + - - +
42C HIS 3.4 0.8 - - - -
43C ALA* 1.3 78.1 - - + +
45C SER* 1.3 60.3 + - - +
46C GLY* 3.6 0.6 + - - -
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C MET* 5.4 5.2 - - - +
41C GLN* 3.7 13.9 + - - -
42C HIS* 3.6 11.8 + - - -
43C ALA 3.1 0.8 - - - -
44C LYS* 1.3 78.9 - - - +
46C GLY* 1.3 58.1 + - - +
47C GLU* 4.8 7.9 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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