Contacts of the helix formed by residues 26 - 30 (chain S) in PDB entry 3H1I
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 PHE 26 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313P GLN* 4.4 7.4 - - - -
318P PHE* 3.6 41.1 - + + -
378P LEU* 4.1 16.8 - - + -
21S TYR* 3.7 35.2 - + - -
24S ALA* 3.2 26.0 + - + -
25S GLY* 1.3 72.6 - - - +
27S ASN* 1.3 72.4 + - - +
28S LYS 2.9 5.6 - - - -
29S TYR* 2.8 29.5 + - - +
30S GLY 3.5 2.4 + - - -
31S LEU* 3.2 28.7 + - + +
33S ARG* 3.5 36.8 - - + -
36S THR* 3.9 15.7 - - + -
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Residues in contact with ASN 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S TYR* 3.0 42.1 - - + +
22S ASN* 4.4 12.0 + - - +
25S GLY* 3.3 21.0 - - - -
26S PHE* 1.3 82.4 - - - +
28S LYS* 1.3 64.5 + - - +
29S TYR 3.1 1.6 - - - -
30S GLY 3.1 8.0 + - - +
31S LEU 3.8 11.0 - - - -
80S TRP* 3.3 27.6 - - - +
81S VAL* 2.7 42.3 + - + +
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Residues in contact with LYS 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S ASN 3.3 25.1 + - - -
23S ALA 4.8 1.4 + - - -
25S GLY* 3.3 25.0 - - - +
26S PHE 2.9 1.6 - - - -
27S ASN* 1.3 82.8 + - - +
29S TYR* 1.3 61.0 + - + +
30S GLY 3.2 1.6 - - - -
74S ILE* 3.4 23.5 - - + +
75S LEU* 3.1 32.6 + - - +
80S TRP* 3.6 50.2 - - + -
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Residues in contact with TYR 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P LEU* 4.3 12.9 - - + +
317P THR* 5.8 1.8 - - + -
318P PHE* 4.2 26.2 - + - -
3007P PEE 3.3 29.8 + - - -
25S GLY 4.4 6.5 - - - -
26S PHE 2.8 13.0 + - - +
28S LYS* 1.3 80.2 - - + +
30S GLY* 1.3 59.7 + - - +
31S LEU* 3.9 17.0 - - + +
64S ARG* 2.9 20.1 + - - -
65S ALA* 3.7 14.8 - - + +
68S LEU* 3.4 29.3 - - + +
69S SER* 3.8 31.6 + - - -
72S HIS* 5.9 1.2 - - - -
73S ARG 3.8 11.3 + - - -
74S ILE* 4.7 11.6 - - + +
75S LEU* 3.3 8.0 - - - +
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Residues in contact with GLY 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27S ASN 3.1 14.0 + - - -
28S LYS 3.2 0.8 - - - -
29S TYR* 1.3 81.2 - - - +
31S LEU* 1.3 59.6 + - - +
32S MET* 5.3 0.2 - - - +
61S ARG* 4.0 13.0 - - - +
64S ARG* 3.4 19.8 + - - -
75S LEU* 3.3 16.2 - - - +
79S GLN 4.5 2.9 - - - -
81S VAL* 3.8 16.5 - - - +
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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