Contacts of the strand formed by residues 2 - 11 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3J ILE* 4.4 10.3 - - - -
40J GLU 3.9 8.3 - - - +
41J ASP* 4.0 6.1 - - - +
43J VAL* 3.9 13.2 - - + +
96J GLN* 3.2 49.8 - - + +
3K ILE* 1.3 87.0 + - - +
4K ARG* 3.5 42.0 - - - +
96K GLN* 3.4 10.6 - - - +
97K THR 2.9 41.0 + - - +
98K ASP* 5.1 5.2 + - - +
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Residues in contact with ILE 3 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J ILE* 4.1 22.0 - - + -
43J VAL* 3.3 33.3 - - + +
2K MET* 1.3 85.1 - - - +
4K ARG* 1.3 65.2 + - - +
43K VAL* 3.8 19.1 - - + -
94K THR* 3.4 32.3 - - + -
95K VAL 3.3 3.4 - - - +
96K GLN* 3.5 32.8 - - + +
2L MET* 4.5 6.3 - - - -
3L ILE* 4.2 19.1 - - + -
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Residues in contact with ARG 4 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J GLU* 3.0 31.9 + - - +
42J VAL 3.9 7.9 + - - -
43J VAL* 4.0 9.0 - - - +
2K MET* 3.5 36.5 - - + +
3K ILE* 1.3 78.4 + - - +
5K GLY* 1.3 67.1 + - - +
6K ILE* 5.5 0.2 - - + -
93K MET 3.8 0.3 - - - +
94K THR* 3.5 1.3 - - - -
95K VAL* 2.8 35.2 + - + +
97K THR* 3.6 24.2 + - + +
98K ASP 5.9 0.2 - - - -
99K VAL 3.7 21.7 + - - -
100K PRO* 5.4 1.4 - - - +
101K GLN* 3.8 42.0 + - - +
104K ILE* 4.2 12.3 - - + -
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Residues in contact with GLY 5 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J VAL* 3.0 21.6 + - - +
44J GLN* 3.8 9.2 - - - -
72J PRO* 3.2 18.7 - - - +
4K ARG* 1.3 77.3 - - - +
6K ILE* 1.3 62.5 + - - +
92K MET* 3.7 15.9 - - - -
93K MET 3.4 7.4 - - - -
104K ILE* 4.2 4.7 - - - +
106K HIS* 3.7 5.2 + - - -
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Residues in contact with ILE 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K ARG 4.6 0.9 - - - +
5K GLY* 1.3 76.0 - - - -
7K ARG* 1.3 64.8 + - - +
31K ILE* 3.8 21.0 - - + +
35K ASN* 3.8 28.9 - - + +
37K THR* 4.2 4.9 - - - +
91K VAL* 3.6 3.1 - - - +
92K MET* 3.4 4.4 - - - +
93K MET* 2.7 45.1 + - + +
95K VAL* 3.5 37.0 - - + -
104K ILE* 3.7 18.8 - - + -
105K ARG 3.7 23.6 - - - +
106K HIS* 3.9 2.7 - - + -
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Residues in contact with ARG 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72J PRO* 3.9 23.3 - - + -
73J VAL* 3.5 27.1 + - - +
74J THR* 4.0 13.4 + - - -
6K ILE* 1.3 76.8 - - - +
8K GLY* 1.3 76.1 + - - +
9K ALA* 4.1 5.3 - - - +
31K ILE* 4.2 4.2 - - - +
90K ARG* 3.6 28.5 - - - +
91K VAL 3.2 18.5 + - - +
92K MET* 3.9 15.5 - - + -
106K HIS* 3.1 23.5 - - + -
107K VAL 3.0 20.8 + - - -
108K TYR* 3.5 28.3 + - - +
115K LEU* 5.4 1.8 - - - +
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Residues in contact with GLY 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ARG* 1.3 84.8 + - - +
9K ALA* 1.3 61.8 + - - +
27K LEU* 4.1 2.7 - - - -
31K ILE* 3.9 9.0 - - - -
90K ARG* 3.4 0.2 - - - -
91K VAL* 3.0 42.0 + - - +
107K VAL 3.0 13.5 - - - -
108K TYR* 4.5 2.2 - - - -
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Residues in contact with ALA 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ARG* 4.1 4.0 - - - +
8K GLY* 1.3 74.5 - - - +
10K THR* 1.3 65.2 + - - +
27K LEU* 3.7 9.6 - - - +
88K CYS* 4.4 2.2 - - - -
89K ILE 3.2 13.0 - - - +
90K ARG* 4.0 14.6 - - + -
107K VAL 3.0 6.3 + - - -
108K TYR* 3.6 12.6 - - + -
109K LEU 2.9 25.3 + - - -
112K ALA* 3.8 19.7 - - + -
115K LEU* 4.2 5.8 - - + -
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Residues in contact with THR 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K ALA* 1.3 77.2 - - - +
11K THR* 1.3 65.2 + - - +
23K LYS* 3.9 36.7 + - + +
24K THR 4.6 0.4 - - - +
27K LEU* 3.9 20.4 - - + -
88K CYS* 3.4 6.7 - - - -
89K ILE* 2.8 49.6 + - + +
109K LEU* 3.5 18.6 - - - +
110K GLU* 3.6 18.2 - - - +
112K ALA* 4.5 0.4 - - - -
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Residues in contact with THR 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K THR* 1.3 83.1 + - - +
12K VAL* 1.3 71.2 + - - +
23K LYS* 4.1 7.6 + - - +
85K LEU* 3.9 23.8 - - + -
86K LYS 3.9 11.0 - - - +
87K LYS* 3.1 13.0 - - - +
88K CYS* 4.3 2.9 - - + -
110K GLU* 3.1 20.9 - - - +
111K LYS* 2.9 46.9 + - + +
112K 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