Contacts of the helix formed by residues 27 - 31 (chain M) in PDB entry 1W72
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 ASN 27 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ASN* 4.8 10.7 + - - -
25M GLY 3.1 0.2 + - - -
26M ASN* 1.3 76.9 - - - +
28M ILE* 1.3 62.9 + - - +
29M GLY* 3.0 2.9 - - - -
30M SER* 2.7 39.8 + - - +
31M ARG* 2.8 8.5 + - - +
68M GLY* 3.6 9.3 - - - +
69M ASN* 2.9 18.3 + - - +
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Residues in contact with ILE 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M TYR* 3.7 11.0 - - - +
4M LEU* 3.7 23.3 - - + -
23M CYS* 3.3 27.8 - - - +
25M GLY 3.2 9.1 + - - +
26M ASN 3.0 2.2 + - - -
27M ASN* 1.3 77.0 - - - +
29M GLY* 1.3 60.0 + - - +
31M ARG* 2.9 22.7 + - - +
33M VAL* 3.8 16.8 - - + -
66M ASN* 3.0 22.0 + - - +
68M GLY 3.2 0.4 + - - +
69M ASN 3.4 5.6 - - - +
70M MET* 3.2 32.8 - - - +
71M ALA* 3.7 15.5 - - + -
90M VAL* 4.2 10.3 - - + -
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Residues in contact with GLY 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ARG* 3.0 16.9 + - - -
89D GLU* 5.6 0.3 - - - +
27M ASN* 3.0 0.8 - - - -
28M ILE* 1.3 79.1 - - - +
30M SER* 1.3 56.4 + - - +
31M ARG 3.6 4.3 + - - +
51M ASP* 5.1 2.1 - - - +
66M ASN* 3.3 19.4 + - - +
67M SER* 3.9 13.2 - - - -
68M GLY 2.9 19.0 + - - -
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Residues in contact with SER 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLY* 4.0 19.4 - - - +
82D ARG* 3.3 30.6 + - - +
83D GLY* 4.4 23.0 - - - -
87D GLN 5.6 1.1 - - - -
27M ASN* 2.7 30.2 + - - +
29M GLY* 1.3 76.2 - - - +
31M ARG* 1.3 71.4 + - - +
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Residues in contact with ARG 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ARG* 5.3 0.3 + - - -
83D GLY* 6.4 0.6 - - - -
100I TYR* 6.1 0.7 - - - -
2M TYR* 3.2 36.8 + - - -
26M ASN 3.0 15.2 + - - -
27M ASN* 2.8 30.3 + - - +
28M ILE* 2.9 9.2 + - - +
29M GLY 3.9 2.4 - - - +
30M SER* 1.3 88.6 + - - +
32M SER* 1.3 60.4 + - - +
33M VAL 3.9 0.2 - - - -
51M ASP* 3.6 4.0 - - - +
66M ASN* 3.1 21.0 + - - -
90M VAL* 3.9 29.4 - - + -
91M TRP 4.1 10.8 - - - +
92M ASP* 2.9 29.2 + - - -
94M ARG* 6.0 1.8 - - - +
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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