Contacts of the helix formed by residues 22 - 31 (chain A) in PDB entry 6W6Y
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 ASP 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA* 1.3 72.6 - - - +
23A ILE* 1.3 65.8 + - - +
24A VAL* 2.9 26.2 + - - +
25A GLU* 3.0 29.4 + - + +
26A GLU* 3.0 21.1 + - - +
52A ALA* 5.1 0.4 - - - +
156A PHE* 3.8 28.4 - - + -
201A AMP 3.0 25.4 + - - -
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Residues in contact with ILE 23 (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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21A ALA 3.5 0.8 + - - -
22A ASP* 1.3 71.0 - - - +
24A VAL* 1.3 60.6 + - + +
26A GLU* 3.6 2.4 - - - +
27A ALA* 2.8 28.4 + - - +
35A VAL* 4.0 13.5 - - + -
36A VAL 3.9 11.0 - - - +
49A VAL* 4.3 14.6 - - + -
52A ALA* 5.5 0.2 - - + -
53A LEU* 4.2 16.2 - - + -
123A LEU* 3.9 16.2 - - + -
124A ALA* 3.7 10.1 - - - +
125A PRO* 3.7 37.5 - - + -
154A ALA* 3.9 13.2 - - + -
201A AMP 2.9 37.1 + - + +
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Residues in contact with VAL 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 ASP* 2.9 20.6 + - - +
23A ILE* 1.3 74.3 - - + +
25A GLU* 1.3 70.1 + - - +
27A ALA* 3.3 6.6 + - - +
28A LYS* 3.1 42.4 + - - +
52A ALA* 3.6 38.1 - - + +
53A LEU* 4.1 13.9 - - + +
56A ALA* 3.5 24.9 - - + -
88A LEU* 4.5 3.8 - - + +
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Residues in contact with GLU 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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21A ALA* 6.1 0.7 - - + -
22A ASP* 3.0 30.2 + - + +
24A VAL* 1.3 78.6 - - - +
26A GLU* 1.3 63.9 + - - +
28A LYS* 3.0 39.6 + - - +
29A LYS* 3.0 30.4 + - - +
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Residues in contact with GLU 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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7A SER 4.5 0.2 - - - +
9A TYR* 2.6 37.0 + - - +
19A LYS* 2.7 32.7 + - - -
21A ALA* 3.7 24.5 - - + +
22A ASP 3.0 8.9 + - - +
23A ILE* 3.6 8.1 - - - +
25A GLU* 1.3 76.7 - - - +
27A ALA* 1.3 58.1 + - - +
29A LYS* 3.2 11.5 + - - +
30A VAL* 2.8 49.1 + - + +
123A LEU* 3.9 17.0 - - + -
154A ALA* 4.4 5.8 - - + -
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Residues in contact with ALA 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 ILE 2.8 18.1 + - - +
24A VAL* 3.6 6.3 - - - +
25A GLU 3.3 0.6 - - - -
26A GLU* 1.3 76.7 - - - +
28A LYS* 1.3 57.2 + - - +
31A LYS* 2.9 26.5 + - - +
32A PRO* 3.9 5.4 - - + -
35A VAL* 4.7 6.7 - - + -
53A LEU* 5.5 0.7 - - + -
87A ASN 5.5 0.2 - - - +
88A LEU* 3.4 45.2 - - + +
123A LEU* 3.6 15.8 - - + +
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Residues in contact with LYS 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 VAL* 3.1 28.9 + - + +
25A GLU* 3.0 39.1 + - - +
26A GLU 3.2 0.2 - - - -
27A ALA* 1.3 76.6 - - - +
29A LYS* 1.3 62.3 + - - +
31A LYS* 4.0 12.1 - - - +
56A ALA* 5.7 2.7 - - + +
87A ASN* 5.4 11.4 - - - +
88A LEU* 4.1 16.8 - - + -
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Residues in contact with LYS 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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3A VAL* 5.7 0.2 - - - +
5A SER* 3.8 21.9 + - - +
7A SER* 2.8 35.7 + - - +
19A LYS* 4.4 10.4 - - - +
25A GLU 3.0 17.1 + - - +
26A GLU* 3.8 17.9 - - - +
28A LYS* 1.3 78.3 - - - +
30A VAL* 1.3 64.3 + - + +
31A LYS* 4.3 6.6 - - - +
169B LEU* 6.6 0.4 - - - -
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Residues in contact with VAL 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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3A VAL* 3.6 9.4 - - - +
4A ASN* 3.3 15.5 + - - -
5A SER* 3.6 32.7 + - - +
6A PHE* 3.5 42.4 - - + -
26A GLU* 2.8 45.8 + - + +
29A LYS* 1.3 76.9 - - + +
31A LYS* 1.3 69.3 + - - +
32A PRO* 3.9 11.4 - - + -
123A LEU* 5.3 0.4 - - + -
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Residues in contact with LYS 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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3A VAL* 2.7 55.4 + - + +
27A ALA 2.9 13.8 + - - +
28A LYS* 4.0 16.4 - - - +
29A LYS 4.3 5.2 - - - +
30A VAL* 1.3 77.6 - - - +
32A PRO* 1.3 68.1 - - - +
88A LEU 4.4 4.0 - - - -
89A ALA* 5.0 1.3 - - - +
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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