Contacts of the strand formed by residues 88 - 94 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F ALA* 4.4 2.5 - - - -
10F THR 3.5 13.5 - - - +
11F THR* 4.3 0.4 - - + -
49F ALA* 3.5 2.8 - - - -
50F THR* 3.1 32.9 + - + +
53F LEU* 4.2 0.4 - - - +
85F LEU* 3.7 41.7 - - + +
86F LYS 3.8 4.0 - - - +
87F LYS* 1.3 78.3 - - - +
89F ILE* 1.3 64.3 + - - +
90F ARG* 3.8 34.7 + - - +
115F LEU* 4.3 7.4 - - - -
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Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ALA* 3.3 4.2 - - - +
10F THR* 3.1 43.3 + - + +
12F VAL* 3.8 24.0 - - + -
20F ILE* 3.8 22.7 - - + +
24F THR* 3.7 23.8 - - + +
27F LEU* 4.3 4.3 - - + +
47F LEU* 4.3 13.7 - - + -
48F SER 3.3 11.4 - - - +
49F ALA* 4.6 0.7 - - + -
53F LEU* 3.8 17.7 - - + -
58F PRO* 4.2 24.7 - - + -
87F LYS 5.0 0.4 - - - +
88F CYS* 1.3 74.1 - - - +
90F ARG* 1.3 61.1 + - - +
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Residues in contact with ARG 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E PHE* 4.2 18.7 - - - -
74E THR* 4.2 11.4 - - + +
7F ARG* 3.7 27.8 - - - +
8F GLY 3.4 4.3 - - - -
9F ALA* 4.4 2.5 - - + -
46F LEU 3.8 0.3 - - - +
47F LEU* 3.2 5.7 - - - +
48F SER* 2.8 47.7 + - - +
50F THR* 3.8 13.7 - - - +
78F GLU* 3.3 44.3 + - - +
85F LEU* 4.5 10.3 + - - +
88F CYS* 3.8 26.5 + - - +
89F ILE* 1.3 77.7 - - - +
91F VAL* 1.3 61.4 + - - +
115F LEU* 3.8 28.9 - - - +
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Residues in contact with VAL 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E THR* 6.1 0.4 - - - -
6F ILE 4.3 0.4 - - - +
7F ARG* 3.2 12.3 + - - -
8F GLY* 3.0 36.9 + - - +
27F LEU* 3.7 15.0 - - + -
28F LEU* 4.4 10.3 - - + -
31F ILE* 3.6 27.8 - - + -
45F MET* 3.8 32.5 - - + -
46F LEU 3.3 5.4 - - - +
47F LEU* 4.1 12.6 - - + -
90F ARG* 1.3 74.6 - - - +
92F MET* 1.3 65.4 + - - +
93F MET* 4.0 7.2 - - + +
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Residues in contact with MET 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E GLN* 3.6 39.7 - - - +
45E MET 5.0 0.9 - - - +
46E LEU* 4.6 8.3 - - + -
72E PRO* 3.8 20.9 - - + +
74E THR* 4.4 22.2 - - + -
5F GLY* 3.6 12.6 - - - -
6F ILE 3.3 47.8 - - - +
7F ARG* 3.8 13.7 - - + -
44F GLN 4.2 0.3 - - - +
45F MET* 3.6 1.7 - - - -
46F LEU* 3.0 42.2 + - + +
76F MET* 6.0 0.2 - - + -
91F VAL* 1.3 73.2 - - - +
93F MET* 1.3 59.5 + - - +
94F THR* 4.2 1.7 + - - +
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Residues in contact with MET 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F ARG 3.8 0.2 - - - +
5F GLY* 3.3 3.6 - - - -
6F ILE* 2.8 43.9 + - + +
28F LEU* 3.7 22.9 - - + -
31F ILE* 3.9 26.7 - - + -
32F ILE* 5.1 3.4 - - + -
37F THR* 4.4 10.1 - - - -
42F VAL* 3.8 18.8 - - + -
44F GLN 3.8 2.2 - - - -
45F MET* 3.7 30.3 - - + +
68F TRP* 3.7 18.4 - - + -
91F VAL* 4.0 8.5 - - + -
92F MET* 1.3 74.3 - - - +
94F THR* 1.3 62.7 + - - +
95F VAL* 4.0 16.3 + - + -
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Residues in contact with THR 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 4.9 2.5 - - + -
94D THR* 6.3 0.2 - - + -
3E ILE* 5.9 0.2 - - + -
43E VAL* 4.1 7.2 - - + -
44E GLN* 2.7 32.7 + - - +
94E THR* 6.3 1.1 - - + -
3F ILE* 3.4 28.9 - - + -
4F ARG 3.6 2.7 - - - -
42F VAL* 3.4 5.7 - - - +
43F VAL* 2.7 43.8 + - + -
44F GLN* 3.0 25.9 + - + +
92F MET 4.6 2.3 + - - -
93F MET* 1.3 70.2 - - - +
95F VAL* 1.3 59.8 + - - +
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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