Contacts of the strand formed by residues 2 - 11 (chain G) 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 MET 2 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G ILE* 1.3 92.1 + - - +
4G ARG* 3.3 44.4 - - - +
96G GLN* 3.5 10.8 - - - +
97G THR 2.8 42.0 + - - +
98G ASP* 4.0 14.9 + - - +
3I ILE* 4.3 7.0 - - - -
40I GLU 3.8 8.5 - - - +
41I ASP* 4.0 20.4 - - - +
43I VAL* 4.0 5.4 - - + -
96I GLN* 3.7 40.4 - - + +
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Residues in contact with ILE 3 (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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2G MET* 1.3 92.2 - - - +
4G ARG* 1.3 59.9 + - - +
43G VAL* 3.5 15.9 - - + -
94G THR* 3.3 33.4 - - + -
95G VAL 3.5 2.5 - - - +
96G GLN* 3.9 10.8 - - - -
2H MET* 3.3 33.2 - - + -
3H ILE* 4.0 23.6 - - + -
3I ILE* 4.1 15.7 - - + +
43I VAL* 3.2 34.5 - - + +
94I THR* 6.2 0.2 - - + -
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Residues in contact with ARG 4 (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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2G MET* 3.3 34.9 - - + +
3G ILE* 1.3 78.6 + - - +
5G GLY* 1.3 62.2 + - - +
6G ILE* 5.8 0.2 - - + -
94G THR* 3.5 2.1 - - - -
95G VAL* 2.9 35.4 + - + +
97G THR* 3.5 30.1 - - + +
99G VAL 3.6 17.3 + - - -
100G PRO* 5.1 2.2 - - - +
101G GLN* 3.8 38.2 + - - +
104G ILE* 4.3 13.5 - - + -
40I GLU* 3.1 31.3 + - - +
42I VAL 3.6 15.4 + - - -
43I VAL* 3.9 10.3 - - - -
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Residues in contact with GLY 5 (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* 1.3 76.7 - - - +
6G ILE* 1.3 64.0 + - - +
92G MET* 3.5 17.9 - - - -
93G MET 3.3 7.4 - - - -
104G ILE* 4.0 5.5 - - - +
106G HIS* 3.6 9.4 + - - -
43I VAL 3.0 16.4 + - - -
44I GLN* 3.7 9.6 - - - -
72I PRO* 3.4 14.8 - - - +
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Residues in contact with ILE 6 (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 5.3 0.2 - - - -
5G GLY* 1.3 74.6 - - - -
7G ARG* 1.3 65.0 + - - +
31G ILE* 3.7 17.9 - - + +
35G ASN* 3.7 34.1 - - + +
37G THR* 4.3 4.7 - - - +
91G VAL* 3.8 1.9 - - - +
92G MET* 3.3 6.3 - - - +
93G MET* 2.8 44.8 + - + +
95G VAL* 3.6 37.5 - - + -
104G ILE* 3.6 21.1 - - + -
105G ARG 3.6 24.0 - - - +
106G HIS* 3.8 3.1 - - + -
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Residues in contact with ARG 7 (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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6G ILE* 1.3 78.0 - - - +
8G GLY* 1.3 79.7 + - - +
9G ALA* 4.1 4.6 - - - +
31G ILE* 4.3 3.6 - - - +
90G ARG* 3.4 26.6 - - - +
91G VAL* 2.7 32.1 + - - +
92G MET* 3.8 31.0 - - + +
106G HIS* 3.1 23.1 - - + -
107G VAL 3.0 20.0 + - - -
108G TYR* 4.2 24.0 + - - +
115G LEU* 5.4 0.8 - - - +
72I PRO* 4.0 15.3 - - + -
73I VAL 3.3 21.6 + - - +
74I THR* 3.8 19.8 + - - +
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Residues in contact with GLY 8 (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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7G ARG* 1.3 90.5 + - - +
9G ALA* 1.3 60.5 + - - -
27G LEU* 3.9 6.1 - - - -
31G ILE* 4.3 1.6 - - - -
90G ARG* 3.4 0.3 - - - -
91G VAL* 2.9 40.2 + - - +
107G VAL 3.0 16.6 - - - -
108G TYR* 4.3 3.6 - - - -
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Residues in contact with ALA 9 (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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7G ARG* 4.1 6.1 - - - +
8G GLY* 1.3 76.0 - - - +
10G THR* 1.3 55.4 + - - +
27G LEU* 3.5 7.4 - - - +
88G CYS* 4.4 2.9 - - - -
89G ILE 3.3 12.3 - - - +
90G ARG* 4.1 6.7 - - + -
107G VAL 2.9 6.3 + - - +
108G TYR* 3.4 20.9 - - + -
109G LEU 2.8 30.8 + - - -
112G ALA* 3.7 5.4 - - + -
115G LEU* 3.6 18.6 - - + -
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Residues in contact with THR 10 (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* 1.3 76.3 - - - +
11G THR* 1.3 69.9 + - - +
23G LYS* 3.9 36.2 + - + +
24G THR 4.6 1.1 - - - +
26G GLN* 5.5 0.7 + - - -
27G LEU* 4.1 16.8 - - + -
88G CYS* 3.5 5.7 - - - -
89G ILE* 3.0 45.2 + - + +
109G LEU* 3.3 29.4 - - - +
110G GLU* 3.5 11.6 - - - +
112G ALA* 4.0 1.3 - - - -
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Residues in contact with THR 11 (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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10G THR* 1.3 84.5 + - - +
12G VAL* 1.3 68.9 + - - +
23G LYS* 3.5 25.1 + - - +
85G LEU* 3.7 41.1 - - + -
86G LYS 4.0 8.5 - - - +
87G LYS 3.5 7.0 - - - +
88G CYS* 4.3 1.1 - - - -
89G ILE* 5.7 0.2 - - - -
110G GLU* 3.1 11.5 - - - +
111G LYS* 3.0 38.0 + - + +
112G ALA 4.0 3.4 - - - +
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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