Contacts of the strand formed by residues 19 - 25 (chain Y) in PDB entry 3HI6
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 VAL 19 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Y LEU* 3.7 31.6 - - + -
13Y ALA* 3.7 29.4 - - + -
17Y ASP 4.0 6.7 - - - +
18Y ARG* 1.3 79.6 - - - +
20Y THR* 1.3 65.7 + - - +
21Y ILE* 4.4 8.7 - - + -
73Y LEU 3.9 0.6 - - - +
74Y THR* 3.3 9.2 - - - +
75Y ILE* 2.9 55.5 + - + +
78Y LEU* 4.0 19.3 - - + -
103Y VAL* 4.8 2.2 - - + -
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Residues in contact with THR 20 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y SER 4.9 0.2 - - - +
8Y PRO* 4.4 10.0 - - - +
11Y LEU* 4.4 5.0 - - - +
18Y ARG* 5.2 5.2 + - - +
19Y VAL* 1.3 77.1 + - - +
21Y ILE* 1.3 67.4 + - - +
22Y THR* 4.3 12.1 - - + +
72Y THR* 4.0 15.7 - - + +
73Y LEU 3.6 3.6 - - - -
74Y THR* 3.8 15.9 + - - +
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Residues in contact with ILE 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Y GLN* 4.0 10.5 - - - +
7Y SER 3.6 8.3 - - - +
8Y PRO* 4.6 0.4 - - + -
11Y LEU* 4.1 14.4 - - + -
19Y VAL* 4.5 7.2 - - + -
20Y THR* 1.3 78.3 - - - +
22Y THR* 1.3 71.7 + - - +
35Y TRP* 3.9 8.9 - - + -
72Y THR* 3.3 4.2 - - - +
73Y LEU* 2.9 49.4 + - + +
75Y ILE* 5.5 3.4 - - + -
86Y TYR* 4.0 29.4 - - + -
101Y THR* 3.4 38.8 - - + +
103Y VAL* 4.3 7.4 - - + -
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Residues in contact with THR 22 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y THR 4.5 0.4 - - - -
6Y GLN* 3.4 7.6 - - - +
7Y SER* 2.7 58.7 + - - +
20Y THR* 4.3 16.2 - - + +
21Y ILE* 1.3 78.8 - - - +
23Y CYS* 1.3 61.9 + - - +
35Y TRP* 4.3 0.7 - - - -
71Y PHE 3.4 7.2 - - - -
72Y THR* 4.2 13.0 - - - +
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Residues in contact with CYS 23 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y MET* 3.3 25.6 - - - -
5Y THR 3.4 6.3 - - - -
6Y GLN* 4.2 0.2 - - - +
22Y THR* 1.3 78.8 - - - +
24Y ARG* 1.3 60.4 + - - +
33Y LEU* 4.1 5.8 - - - -
35Y TRP* 3.5 18.6 - - + -
69Y THR 3.7 1.9 - - - +
70Y ASP* 3.7 1.3 - - - +
71Y PHE* 2.9 36.3 + - + +
88Y CYS* 2.1 49.6 - - + -
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Residues in contact with ARG 24 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Y GLN 3.7 0.9 - - - +
4Y MET* 3.4 4.9 - - - -
5Y THR* 2.6 56.4 + - + +
23Y CYS* 1.3 75.0 - - - +
25Y ALA* 1.3 65.1 + - - +
69Y THR* 3.3 16.5 - - + +
70Y ASP* 2.9 43.8 + - - +
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Residues in contact with ALA 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y ILE* 4.7 1.1 - - + -
3Y GLN 3.5 5.4 - - - -
4Y MET* 3.6 24.9 - - + +
24Y ARG* 1.3 78.0 - - - +
26Y SER* 1.3 61.5 + - - +
27Y GLN 3.1 21.1 + - - +
29Y ILE* 4.0 18.6 - - + -
69Y THR* 2.8 34.3 + - - +
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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