Contacts of the strand formed by residues 88 - 94 (chain H) in PDB entry 2CHS
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 CYS 88 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ALA* 4.5 7.6 - - - -
10H THR 3.3 10.1 - - - -
11H THR* 4.2 0.7 - - - -
48H SER 4.0 0.3 - - - +
49H ALA* 3.6 4.5 - - - +
50H THR* 3.2 28.7 + - + +
53H LEU* 4.3 0.9 - - - +
85H LEU* 3.5 42.8 - - + +
86H LYS 4.0 3.8 - - - +
87H LYS* 1.3 75.6 - - - +
89H ILE* 1.3 71.9 + - - +
90H ARG* 3.3 35.9 + - - +
115H LEU* 5.8 0.2 - - - -
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Residues in contact with ILE 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ALA* 3.3 3.6 - - - +
10H THR* 2.8 46.6 + - + +
12H VAL* 4.1 18.2 - - + -
20H ILE* 3.9 22.2 - - + +
24H THR* 3.7 27.1 - - + +
27H LEU* 5.1 4.5 - - + -
47H LEU* 4.8 9.0 - - + -
48H SER 3.4 11.4 - - - +
49H ALA* 4.9 1.1 - - + -
53H LEU* 3.9 21.5 - - + -
58H PRO* 4.3 18.2 - - + -
87H LYS 5.0 0.2 - - - +
88H CYS* 1.3 79.8 - - - +
90H ARG* 1.3 70.4 + - - +
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Residues in contact with ARG 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G PHE* 4.1 19.8 - - - -
74G THR* 4.0 13.9 + - + +
7H ARG* 3.2 29.9 - - - +
8H GLY 3.4 4.3 - - - -
9H ALA* 4.0 6.4 - - + +
27H LEU* 5.1 0.2 - - - -
46H LEU 4.0 0.3 - - - +
47H LEU* 3.4 8.9 - - - +
48H SER* 3.0 44.1 + - - +
50H THR* 4.0 6.9 - - - +
78H GLU* 3.2 38.9 + - - +
85H LEU* 4.6 12.5 + - - +
88H CYS* 3.3 35.2 + - - +
89H ILE* 1.3 80.2 - - - +
91H VAL* 1.3 60.6 + - - +
115H LEU* 5.1 11.3 - - - +
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Residues in contact with VAL 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G THR* 5.9 0.7 - - - -
6H ILE 4.1 0.4 - - - +
7H ARG* 3.0 24.5 + - - -
8H GLY* 3.0 18.7 + - - -
27H LEU* 3.5 27.1 - - + -
28H LEU* 4.3 8.3 - - + -
31H ILE* 3.5 23.3 - - + -
45H MET* 4.0 28.3 - - + -
46H LEU 3.5 4.0 - - - -
47H LEU* 3.6 15.3 - - + -
90H ARG* 1.3 74.2 - - - +
92H MET* 1.3 62.0 + - - +
93H MET* 3.9 15.0 - - + +
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Residues in contact with MET 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G GLN* 3.8 40.8 - - + +
45G MET 4.1 5.6 - - - +
46G LEU* 4.9 5.4 - - + -
72G PRO* 3.8 25.8 - - - +
73G VAL* 3.7 29.6 - - - -
74G THR* 3.8 22.0 - - + +
5H GLY* 4.3 7.0 - - - -
6H ILE 3.7 2.5 - - - -
7H ARG* 3.8 14.8 - - - -
44H GLN 4.3 0.2 - - - +
45H MET* 3.6 1.6 - - - -
46H LEU* 2.9 47.3 + - + +
76H MET* 5.7 0.4 - - + -
91H VAL* 1.3 73.0 - - - +
93H MET* 1.3 59.9 + - - +
94H THR* 4.0 2.4 + - - +
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Residues in contact with MET 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H ARG 3.9 0.2 - - - +
5H GLY* 3.7 1.1 - - - -
6H ILE* 2.8 43.4 + - + +
28H LEU* 4.1 25.6 - - + -
31H ILE* 4.0 33.2 - - + -
32H ILE* 4.7 5.6 - - + -
37H THR* 4.3 6.7 - - - -
42H VAL* 4.0 18.6 - - + -
44H GLN 4.0 3.1 - - - -
45H MET* 4.2 15.3 - - + -
68H TRP* 4.3 23.1 - - + -
91H VAL* 4.1 7.9 - - + -
92H MET* 1.3 75.5 - - - +
94H THR* 1.3 60.7 + - - +
95H VAL* 4.0 17.8 + - + -
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Residues in contact with THR 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G VAL* 4.1 6.5 - - + -
44G GLN* 2.8 35.2 + - - +
3H ILE* 3.7 30.7 - - + -
4H ARG 3.6 5.6 - - - +
42H VAL* 3.6 1.7 - - - +
43H VAL* 2.8 38.9 + - + -
44H GLN* 3.1 24.7 + - + +
92H MET* 4.6 3.5 + - - +
93H MET* 1.3 71.9 - - - +
95H VAL* 1.3 63.5 + - - +
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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