Contacts of the strand formed by residues 88 - 94 (chain G) in PDB entry 2CHT
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9G ALA* 4.3 9.2 - - - -
10G THR 3.2 18.4 - - - -
11G THR* 4.3 0.7 - - + -
48G SER 3.8 0.3 - - - +
49G ALA* 3.4 4.5 - - - -
50G THR* 3.0 30.5 + - + +
53G LEU* 3.4 1.1 - - - +
85G LEU* 3.5 39.5 - - + +
86G LYS 3.9 3.1 - - - +
87G LYS* 1.3 76.4 - - - +
89G ILE* 1.3 60.5 + - - +
90G ARG* 3.5 38.2 + - - +
115G LEU* 4.6 1.8 - - - -
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Residues in contact with ILE 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G ALA* 3.2 1.9 - - - -
10G THR* 2.8 46.2 + - + +
12G VAL* 3.9 23.8 - - + -
20G ILE* 3.7 23.8 - - + -
24G THR* 3.4 33.0 - - + +
27G LEU* 3.9 6.8 - - + +
47G LEU* 4.7 4.3 - - + -
48G SER 3.2 10.5 - - - +
49G ALA* 4.5 0.2 - - + -
53G LEU* 3.7 17.5 - - + -
58G PRO* 4.1 19.3 - - + -
87G LYS 5.1 0.2 - - - +
88G CYS* 1.3 72.3 - - - +
90G ARG* 1.3 68.3 + - - +
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Residues in contact with ARG 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G ARG* 3.6 13.9 - - - +
8G GLY 3.3 4.5 - - - -
9G ALA* 3.8 10.5 - - + +
27G LEU* 5.1 0.4 - - - -
46G LEU 5.4 0.2 - - - -
47G LEU* 3.3 7.6 - - - +
48G SER* 3.0 42.9 + - - +
50G THR* 3.8 7.1 - - - +
78G GLU* 3.2 38.0 + - - +
85G LEU* 4.9 8.9 + - - +
88G CYS* 3.5 30.6 + - - +
89G ILE* 1.3 75.3 - - - +
91G VAL* 1.3 62.5 + - - +
115G LEU* 4.3 12.3 - - - +
209G TSA 3.0 49.1 + - - -
57I PHE* 3.7 13.9 - - - -
74I THR* 4.2 5.8 - - - +
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Residues in contact with VAL 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE 4.2 3.8 - - - +
7G ARG* 2.8 32.7 + - - -
8G GLY* 2.9 23.6 + - - +
27G LEU* 4.4 7.6 - - + -
28G LEU* 3.8 24.5 - - + -
31G ILE* 3.4 30.1 - - + -
45G MET* 3.9 18.8 - - + -
46G LEU 3.3 11.2 - - - +
47G LEU* 4.1 9.4 - - + -
90G ARG* 1.3 75.9 - - - +
92G MET* 1.3 61.8 + - - +
93G MET* 4.4 4.0 - - + +
74I THR* 5.0 1.5 + - - -
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Residues in contact with MET 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G GLY* 3.5 34.3 - - - -
6G ILE 3.5 13.7 - - - +
7G ARG* 3.6 15.7 - - - -
45G MET* 3.2 4.0 - - - -
46G LEU* 2.8 56.2 + - + +
76G MET* 5.7 0.4 - - + -
91G VAL* 1.3 74.3 - - - +
93G MET* 1.3 60.9 + - - +
94G THR* 3.9 1.7 + - - +
44I GLN* 3.6 33.0 - - - +
45I MET 4.9 2.5 - - - +
46I LEU* 4.8 1.3 - - + -
72I PRO* 3.8 17.7 - - + +
74I THR* 4.0 25.1 - - + -
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Residues in contact with MET 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ARG 3.7 0.2 - - - +
5G GLY* 3.5 0.9 - - - -
6G ILE* 2.8 49.3 + - + +
28G LEU* 4.7 8.7 - - + -
31G ILE* 4.0 25.6 - - + -
32G ILE* 5.1 2.9 - - + -
37G THR* 4.3 15.9 - - - -
42G VAL* 3.8 16.2 - - + -
44G GLN 3.9 1.6 - - - -
45G MET* 3.5 28.3 - - + +
68G TRP* 3.3 38.1 - - + -
91G VAL* 4.5 9.6 - - + -
92G MET* 1.3 75.1 - - - +
94G THR* 1.3 61.1 + - - +
95G VAL* 3.6 7.7 + - + -
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Residues in contact with THR 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G ILE* 3.4 30.3 - - + -
4G ARG 3.5 2.7 - - - -
42G VAL* 3.4 5.9 - - - +
43G VAL* 2.8 48.2 + - + -
44G GLN* 3.0 26.7 + - + +
92G MET* 4.7 3.1 + - - +
93G MET* 1.3 71.0 - - - +
95G VAL* 1.3 56.2 + - - +
3H ILE* 5.2 0.7 - - + -
43I VAL* 4.0 6.5 - - + -
44I GLN* 2.6 36.8 + - - +
94I THR* 6.3 0.9 - - + -
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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