Contacts of the helix formed by residues 22 - 37 (chain A) in PDB entry 2W9Z
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 LEU 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LEU* 1.3 59.7 + - - +
24A ASN* 3.9 25.4 - - + +
25A ASP* 2.7 35.7 + - - +
26A ARG* 2.8 19.4 + - - -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LEU* 1.3 78.2 - - - +
24A ASN* 1.3 68.9 + - - +
25A ASP 3.3 0.7 - - - -
26A ARG* 3.5 37.0 - - + +
27A VAL* 2.8 41.4 + - + +
133B ALA* 5.4 15.3 - - + +
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Residues in contact with ASN 24 (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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22A LEU* 3.9 20.4 - - + +
23A LEU* 1.3 78.3 - - - +
25A ASP* 1.3 52.9 + - - +
27A VAL* 2.9 9.5 - - - +
28A LEU* 2.6 39.5 + - - +
163A HIS* 3.6 30.7 + - + -
166A SER* 4.5 8.1 + - - -
167A LYS* 4.3 13.6 - - - +
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Residues in contact with ASP 25 (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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22A LEU 2.7 36.9 + - - +
24A ASN* 1.3 75.9 - - - +
26A ARG* 1.3 75.7 + - - +
28A LEU* 2.8 12.4 + - + +
29A ARG* 2.6 74.3 + - + +
167A LYS* 5.8 2.0 - - - +
238A LYS* 5.6 4.5 - - - +
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Residues in contact with ARG 26 (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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22A LEU 2.8 28.9 + - - -
23A LEU* 3.3 30.6 + - + +
25A ASP* 1.3 91.0 + - - +
27A VAL* 1.3 66.0 + - + +
29A ARG* 3.7 12.1 + - - +
30A ALA* 3.4 18.4 + - - +
66B PHE* 4.5 11.4 - - + -
130B PHE* 6.3 3.8 - - - -
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Residues in contact with VAL 27 (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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23A LEU* 2.8 43.8 + - + +
24A ASN* 2.9 19.3 - - - +
26A ARG* 1.3 76.5 - - + +
28A LEU* 1.3 59.8 + - - +
30A ALA* 3.2 1.7 + - - +
31A MET* 2.8 40.6 + - + +
163A HIS* 5.9 0.7 - - + -
66B PHE* 4.0 27.1 - - + -
134B ASN* 6.1 0.2 - - - +
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Residues in contact with LEU 28 (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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24A ASN 2.6 23.7 + - - +
25A ASP* 2.8 10.0 + - - +
27A VAL* 1.3 71.3 - - - +
29A ARG* 1.3 61.0 + - + +
31A MET* 3.3 5.6 + - + -
32A LEU* 2.8 44.2 + - + +
155A MET* 5.1 4.5 - - + -
160A PHE* 4.3 25.4 - - + -
163A HIS* 3.5 35.2 - - + +
164A PHE* 6.1 0.2 - - + -
167A LYS* 4.5 5.4 - - - +
236A VAL* 3.4 34.1 - - + +
238A LYS* 3.8 10.8 - - - +
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Residues in contact with ARG 29 (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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25A ASP* 2.6 62.2 + - + +
26A ARG* 3.9 13.3 - - - +
28A LEU* 1.3 73.1 - - + +
30A ALA* 1.3 60.2 + - - +
32A LEU* 3.4 10.8 + - + +
33A LYS* 3.0 46.5 + - - +
238A LYS* 5.4 15.9 - - + +
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Residues in contact with ALA 30 (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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26A ARG 3.4 5.6 + - - +
27A VAL 3.2 8.4 + - - +
28A LEU 3.2 0.2 - - - -
29A ARG* 1.3 78.0 - - - +
31A MET* 1.3 61.3 + - + +
33A LYS* 3.0 9.1 + - - +
34A ALA* 2.7 34.7 + - - +
65B ALA* 3.4 18.1 - - - +
66B PHE* 3.6 41.5 - - + -
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Residues in contact with MET 31 (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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27A VAL* 2.8 29.4 + - + +
28A LEU* 3.8 6.1 - - - +
30A ALA* 1.3 81.5 - - + +
32A LEU* 1.3 59.8 + - - +
34A ALA* 3.8 7.4 - - + +
35A GLU* 3.1 23.7 + - - +
155A MET* 3.4 43.8 - - + +
160A PHE* 4.7 7.3 - - + -
62B ARG* 3.9 43.1 - - + +
65B ALA* 5.0 0.7 - - + -
66B PHE* 3.7 33.0 - - + -
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Residues in contact with LEU 32 (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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28A LEU* 2.8 38.6 + - + +
29A ARG* 3.7 9.0 - - + +
31A MET* 1.3 73.4 - - - +
33A LYS* 1.3 60.8 + - + +
35A GLU* 3.4 30.5 - - - +
36A GLU* 3.6 15.5 + - - +
160A PHE* 4.1 11.0 - - + -
201A SER* 4.0 16.8 - - - +
236A VAL 3.9 6.1 - - - +
237A ILE* 3.8 23.6 - - - +
238A LYS* 3.5 37.7 - - + -
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Residues in contact with LYS 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 ARG* 3.0 38.7 + - - +
30A ALA* 3.0 6.8 + - - +
32A LEU* 1.3 74.4 - - + +
34A ALA* 1.3 56.0 + - - +
35A GLU 2.8 4.7 - - - -
36A GLU* 2.8 42.2 + - - +
37A THR* 3.4 10.2 + - - +
65B ALA* 3.3 25.9 + - + +
66B PHE* 4.4 8.1 + - - +
67B GLU* 3.3 25.7 + - - +
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Residues in contact with ALA 34 (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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30A ALA 2.7 19.0 + - - +
31A MET* 3.8 13.0 - - + +
33A LYS* 1.3 72.7 - - - +
35A GLU* 1.3 58.1 + - - +
37A THR* 2.7 27.6 + - - -
38A CYS* 3.5 13.0 + - - -
151A ASN* 6.2 0.2 - - - +
154A ALA* 5.8 7.0 - - - -
155A MET 5.9 2.5 - - - +
62B ARG* 4.2 20.6 - - + -
65B ALA* 3.4 20.1 - - + +
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Residues in contact with GLU 35 (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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31A MET 3.1 15.8 + - - +
32A LEU* 3.4 19.3 - - - +
33A LYS 2.8 0.2 - - - -
34A ALA* 1.3 75.6 - - - +
36A GLU* 1.3 65.2 + - + +
37A THR 3.1 2.2 - - - -
38A CYS* 3.1 17.5 + - + +
39A ALA* 3.4 12.0 + - - +
154A ALA* 6.0 2.5 - - - -
155A MET* 5.9 1.6 - - + +
160A PHE* 4.1 7.5 - - + -
199A PRO* 3.3 15.9 - - + +
200A PRO* 2.8 28.5 - - + +
201A SER* 2.8 48.5 + - - -
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Residues in contact with GLU 36 (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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32A LEU 3.6 15.6 - - - +
33A LYS* 2.8 18.8 + - - +
35A GLU* 1.3 77.7 - - + +
37A THR* 1.3 61.7 + - + +
38A CYS 3.3 0.4 + - - -
39A ALA* 3.8 17.2 + - - +
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Residues in contact with THR 37 (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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33A LYS 3.6 13.5 - - - +
34A ALA* 2.7 22.5 + - - +
35A GLU 3.1 1.0 - - - -
36A GLU* 1.3 79.8 - - + +
38A CYS* 1.3 58.3 + - - +
39A ALA 3.4 2.3 + - - +
87A ARG* 4.8 2.8 + - - -
151A ASN* 3.3 25.0 + - - -
64B GLU* 5.9 3.1 - - - +
65B ALA* 5.9 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
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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