Contacts of the strand formed by residues 2 - 11 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D ILE* 5.1 2.0 - - - -
40D GLU 4.1 3.4 - - - +
41D ASP 4.0 22.0 - - - +
43D VAL* 4.4 7.0 - - + +
96D GLN* 3.6 43.3 - - + +
3E ILE* 1.3 94.9 + - - +
4E ARG* 3.6 45.1 - - - +
96E GLN* 3.7 5.5 - - - +
97E THR 2.8 37.1 + - - +
98E ASP* 3.7 19.3 + - - -
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Residues in contact with ILE 3 (chain E).
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* 3.3 39.9 - - + -
43D VAL* 3.5 20.9 - - + +
2E MET* 1.3 94.5 - - - +
4E ARG* 1.3 65.8 + - - +
43E VAL* 4.2 8.7 - - + -
94E THR* 4.1 21.5 - - + -
95E VAL 3.1 14.6 - - - +
96E GLN* 3.9 16.2 - - + -
97E THR 4.4 0.4 - - - +
2F MET* 4.9 2.2 - - - -
3F ILE* 3.8 32.5 - - + -
94F THR* 5.9 0.4 - - + -
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Residues in contact with ARG 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLU* 2.9 31.5 + - - +
42D VAL 3.9 5.9 + - - -
43D VAL* 4.0 11.0 - - - +
2E MET* 3.6 35.3 - - + +
3E ILE* 1.3 77.3 - - - +
5E GLY* 1.3 60.6 + - - +
6E ILE* 5.9 0.2 - - + -
93E MET 3.6 0.3 - - - +
94E THR* 3.4 2.3 - - - +
95E VAL* 2.9 36.1 + - + +
97E THR* 4.0 18.3 + - + +
99E VAL 3.3 27.4 + - - -
100E PRO* 5.4 1.4 - - - +
101E GLN* 3.6 39.9 + - + +
104E ILE* 3.9 21.1 - - + -
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Residues in contact with GLY 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL 3.1 16.5 + - - -
44D GLN* 3.6 12.5 - - - +
72D PRO* 3.2 17.8 - - - +
4E ARG* 1.3 75.6 - - - +
6E ILE* 1.3 61.3 + - - +
92E MET* 3.4 19.1 - - - -
93E MET 3.3 6.7 - - - -
104E ILE* 4.1 6.1 - - - +
106E HIS* 3.6 6.6 + - - -
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Residues in contact with ILE 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ARG 4.8 0.7 - - - +
5E GLY* 1.3 73.3 - - - -
7E ARG* 1.3 67.7 + - - +
31E ILE* 4.0 14.4 - - + +
35E ASN* 3.8 23.1 - - + +
37E THR* 3.9 5.6 - - - +
91E VAL* 3.7 2.4 - - - +
92E MET* 3.4 4.9 - - - +
93E MET* 2.7 72.4 + - + +
95E VAL* 3.9 24.9 - - + -
104E ILE* 3.7 22.0 - - + -
105E ARG 3.6 23.3 - - - +
106E HIS* 4.0 2.9 - - + -
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Residues in contact with ARG 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D PRO* 4.0 11.9 - - + -
73D VAL 3.0 30.2 + - - +
74D THR* 3.9 17.1 + - - +
6E ILE* 1.3 77.3 - - - +
8E GLY* 1.3 67.1 + - - +
9E ALA* 4.3 0.6 - - - +
31E ILE* 4.4 3.9 - - - +
90E ARG* 3.6 33.9 - - - +
91E VAL 3.2 20.1 + - - +
92E MET* 3.7 23.3 - - + +
106E HIS* 3.3 24.6 - - + +
107E VAL 3.2 18.4 + - - -
108E TYR* 3.5 36.6 + - - +
115E LEU* 5.4 1.0 - - - +
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Residues in contact with GLY 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ARG* 1.3 81.8 + - - +
9E ALA* 1.3 61.5 + - - +
27E LEU* 4.0 0.9 - - - -
31E ILE* 4.0 7.4 - - - -
90E ARG* 3.2 5.4 - - - +
91E VAL* 2.8 46.1 + - - +
107E VAL 3.0 12.8 - - - -
108E TYR* 4.7 3.1 - - - -
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Residues in contact with ALA 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ARG* 4.3 0.4 - - - +
8E GLY* 1.3 74.5 - - - +
10E THR* 1.3 57.2 + - - +
27E LEU* 3.6 9.0 - - - +
88E CYS* 4.4 1.6 - - - -
89E ILE 3.3 11.4 - - - +
90E ARG* 3.8 14.6 - - + -
107E VAL 2.8 9.2 + - - +
108E TYR* 3.9 16.6 - - + -
109E LEU 2.8 29.8 + - - -
112E ALA* 3.6 19.1 - - + -
115E LEU* 4.0 6.5 - - + -
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Residues in contact with THR 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ALA* 1.3 75.8 - - - +
11E THR* 1.3 71.7 + - - +
23E LYS* 3.7 35.2 + - + +
24E THR* 4.4 1.3 - - - +
27E LEU* 3.7 23.6 - - + -
88E CYS* 3.4 7.6 - - - -
89E ILE* 3.0 43.7 + - + +
109E LEU* 3.6 14.0 + - - +
110E GLU* 3.4 20.4 - - - +
112E ALA* 4.0 2.2 - - - -
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Residues in contact with THR 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E THR* 1.3 88.8 + - - +
12E VAL* 1.3 68.2 + - - +
23E LYS* 3.7 17.2 + - - +
85E LEU* 3.7 30.1 - - + -
86E LYS 3.7 11.0 - - - +
87E LYS 3.1 15.0 - - - +
88E CYS* 4.0 2.0 - - + -
89E ILE 4.8 0.7 - - - +
110E GLU* 3.3 10.4 - - - +
111E LYS* 3.1 41.1 + - + +
112E ALA 4.1 1.6 - - - +
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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