Contacts of the strand formed by residues 22 - 28 (chain A) in PDB entry 1H8O
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A MET* 3.8 26.0 - - + -
16A THR* 3.4 25.4 - - + +
21A ARG* 1.3 78.1 - - - +
23A SER* 1.3 70.3 + - - +
24A ILE* 4.2 7.0 - - + -
77A THR* 3.3 6.4 - - - +
78A ILE* 3.0 38.9 + - + +
81A VAL* 3.2 29.8 - - + -
107A LEU* 4.1 16.4 - - + -
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Residues in contact with SER 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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10A SER* 5.0 0.9 + - - -
11A HIS* 6.0 0.2 - - - -
14A MET* 3.7 14.0 - - - +
21A ARG* 4.1 8.5 + - - -
22A VAL* 1.3 76.4 + - - +
24A ILE* 1.3 64.4 + - - +
25A THR* 3.8 8.9 + - - +
75A THR* 4.1 11.8 - - - +
76A LEU 3.5 2.9 - - - -
77A THR* 2.7 25.1 + - - +
106B LYS* 4.9 15.5 - - - -
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Residues in contact with ILE 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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9A GLN* 4.2 3.8 - - - +
10A SER* 4.6 0.2 - - - +
14A MET* 3.4 20.6 - - + -
22A VAL* 4.5 8.1 - - + -
23A SER* 1.3 72.8 - - - +
25A THR* 1.3 64.0 + - - +
38A TRP* 3.6 22.8 - - + -
75A THR* 3.3 2.6 - - - -
76A LEU* 2.7 55.2 + - + +
78A ILE* 4.6 11.0 - - + -
89A TYR* 3.8 37.5 - - + -
105A THR* 3.7 31.9 - - + +
107A LEU* 5.1 4.7 - - + -
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Residues in contact with THR 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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9A GLN* 3.5 9.9 - - - +
10A SER* 3.1 50.1 + - - -
23A SER* 3.8 9.4 + - - +
24A ILE* 1.3 78.1 - - - +
26A CYS* 1.3 63.5 + - - +
38A TRP* 4.3 0.7 - - - -
74A PHE 3.3 2.9 - - - -
75A THR* 3.6 15.7 - - + +
13B PHE* 3.4 50.6 - - + -
108B GLU* 3.8 6.3 + - - +
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Residues in contact with CYS 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 LEU* 3.6 24.9 - - - -
8A THR 3.3 7.9 - - - +
9A GLN* 4.4 1.1 - - + -
25A THR* 1.3 77.7 - - - +
27A LYS* 1.3 60.6 + - - +
36A VAL* 5.4 1.8 - - - -
38A TRP* 3.7 16.2 - - + -
73A ASP* 3.8 0.5 - - - -
74A PHE* 2.8 42.6 + - + +
91A CYS* 2.0 49.4 - - - -
13B PHE* 4.2 2.6 - - - -
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Residues in contact with LYS 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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6A VAL 3.5 1.7 - - - +
7A LEU* 4.2 2.2 - - - -
8A THR* 2.9 41.7 + - - +
26A CYS* 1.3 75.3 - - - +
28A ALA* 1.3 73.2 + - - +
29A SER* 5.4 1.1 - - - -
72A THR* 3.2 19.1 + - - +
73A ASP* 2.6 33.4 + - - +
11B HIS* 4.2 13.1 + - - -
13B PHE* 4.6 19.7 - - + -
14B MET* 6.3 1.8 - - - +
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Residues in contact with ALA 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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5A ILE* 4.1 2.9 - - + -
6A VAL 3.4 5.8 - - - -
7A LEU* 3.6 19.3 - - + +
26A CYS 4.2 0.4 - - - -
27A LYS* 1.3 84.5 - - - +
29A SER* 1.3 57.9 + - - +
30A GLN 3.1 23.3 - - - +
32A VAL* 3.8 23.6 - - + -
71A GLY 4.7 0.4 - - - +
72A THR* 2.9 28.8 + - - +
74A PHE* 4.7 1.7 - - + -
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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