Contacts of the helix formed by residues 26 - 37 (chain C) in PDB entry 2W4G
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 THR 26 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C LYS 5.2 2.2 - - - +
25C ILE* 1.3 72.6 - - - +
27C LEU* 1.3 59.2 + - - +
28C SER* 2.9 22.0 + - - +
29C GLN* 2.8 52.0 + - - +
30C VAL* 3.0 14.8 + - - +
58C MET* 6.1 0.9 - - - -
62C LYS* 3.7 24.2 - - + +
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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
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26C THR* 1.3 71.8 - - - +
28C SER* 1.3 57.2 + - - +
30C VAL* 3.0 31.1 - - - +
31C GLY 4.3 0.5 + - - -
57C GLU* 3.4 32.9 - - + +
58C MET* 4.3 20.1 - - + +
62C LYS* 3.3 24.0 - - + +
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Residues in contact with SER 28 (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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26C THR* 2.9 18.5 + - - -
27C LEU* 1.3 73.6 - - - +
29C GLN* 1.3 61.6 + - - +
30C VAL 3.0 4.6 + - - -
31C GLY* 3.2 13.5 + - - -
32C ASP* 3.9 8.7 - - - +
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Residues in contact with GLN 29 (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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17C PHE 4.5 12.9 + - - +
18C ASP 5.0 6.6 + - - +
19C ARG* 5.1 11.3 - - - +
25C ILE* 3.2 18.1 - - + +
26C THR* 2.8 45.7 + - - +
28C SER* 1.3 77.2 - - - +
30C VAL* 1.3 57.2 + - - +
31C GLY 3.3 0.4 - - - -
32C ASP* 3.2 14.7 + - + +
33C ILE* 2.9 37.8 + - + +
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Residues in contact with VAL 30 (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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25C ILE* 4.7 0.6 - - - +
26C THR 3.0 17.6 + - - +
27C LEU* 3.0 23.3 - - - +
29C GLN* 1.3 73.0 - - - +
31C GLY* 1.3 62.8 + - - +
33C ILE* 3.6 3.4 + - - +
34C VAL* 3.3 25.1 + - - +
46C ILE* 4.7 9.4 - - + -
57C GLU* 3.4 23.3 - - - +
61C LYS* 3.4 55.8 - - + +
68C PHE* 4.1 6.5 - - + -
71C MET* 5.1 4.0 - - + -
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Residues in contact with GLY 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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27C LEU 4.3 0.6 + - - -
28C SER 3.2 8.7 + - - -
30C VAL* 1.3 80.6 - - - +
32C ASP* 1.3 60.3 + - - +
34C VAL* 4.2 2.6 - - - +
35C ARG* 3.0 34.6 + - - +
43C ASN* 5.4 0.2 - - - -
46C ILE* 3.7 35.2 - - - +
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Residues in contact with ASP 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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28C SER 3.9 12.1 - - - +
29C GLN* 3.2 13.7 + - + +
31C GLY* 1.3 75.3 - - - +
33C ILE* 1.3 66.3 + - + +
34C VAL 3.3 1.3 - - - -
35C ARG* 2.7 56.7 + - - +
36C ALA* 3.8 2.6 + - - +
799M MET* 3.0 36.8 - - + +
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Residues in contact with ILE 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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13C ALA* 6.1 0.9 - - + +
14C PHE* 3.9 18.8 - - + -
17C PHE* 3.9 29.4 - - + -
25C ILE* 3.6 46.9 - - + -
29C GLN* 2.9 24.2 + - + +
30C VAL* 4.2 4.0 - - - +
32C ASP* 1.3 70.9 - - + +
34C VAL* 1.3 63.1 + - - +
35C ARG 3.2 1.2 + - - -
36C ALA* 3.4 5.3 + - - +
37C LEU* 3.2 45.4 + - + +
61C LYS* 5.5 3.4 - - - +
68C PHE* 5.2 3.8 - - + -
72C LEU* 4.9 3.6 - - + -
799M MET* 5.4 2.5 - - + -
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Residues in contact with VAL 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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30C VAL 3.3 16.4 + - - +
31C GLY* 4.2 5.4 - - - +
32C ASP 3.3 0.2 - - - -
33C ILE* 1.3 78.3 - - - +
35C ARG* 1.3 59.5 + - - +
36C ALA 3.5 0.6 + - - -
37C LEU* 3.7 13.8 + - - +
39C GLN 3.5 14.7 - - - +
41C PRO* 4.1 19.7 - - + +
46C ILE* 5.4 1.8 - - + -
61C LYS* 5.7 1.3 - - - +
72C LEU* 3.6 26.6 - - + +
75C ALA* 5.5 7.4 - - + -
79C LYS* 4.7 2.6 + - - -
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Residues in contact with ARG 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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31C GLY* 3.0 23.7 + - - +
32C ASP* 2.7 40.7 + - - +
34C VAL* 1.3 78.1 - - - +
36C ALA* 1.3 58.3 + - - +
37C LEU 5.0 0.2 - - - -
39C GLN 4.5 5.2 + - - -
41C PRO* 4.1 24.9 + - + +
43C ASN* 2.8 38.1 + - - +
46C ILE* 4.8 2.0 - - - +
122C GLU* 5.7 2.8 + - - -
795M ARG* 4.3 31.1 + - - +
796M GLY* 3.9 21.6 - - - +
799M MET* 4.4 14.6 - - + +
800M ARG* 3.4 26.5 + - - +
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Residues in contact with ALA 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 ASP 3.8 2.3 + - - +
33C ILE* 3.4 7.3 + - - +
35C ARG* 1.3 76.5 - - - +
37C LEU* 1.3 62.4 + - + +
38C GLY* 2.7 13.6 + - - -
799M MET* 4.5 6.7 - - + +
800M ARG* 3.8 33.8 - - + +
803M TYR* 4.3 26.5 - - + -
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Residues in contact with LEU 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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10C PHE* 3.6 42.7 - - + -
13C ALA* 4.3 18.8 - - + -
14C PHE* 3.7 18.8 - - + -
33C ILE* 3.2 24.1 + - + +
34C VAL* 3.7 10.4 + - - +
35C ARG 3.5 1.0 - - - -
36C ALA* 1.3 76.9 - - + +
38C GLY* 1.3 57.6 + - - +
39C GLN* 3.1 8.5 + - - +
72C LEU* 3.5 34.8 - - + -
79C LYS* 3.9 10.2 + - - -
803M TYR* 5.0 8.5 - - + -
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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