Contacts of the strand formed by residues 30 - 37 (chain E) in PDB entry 5HJD
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 HIS 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E ALA* 4.9 6.1 - - + -
18E GLN 3.2 12.8 - - - +
19E VAL* 3.3 29.4 - - + +
20E ARG* 3.6 5.9 - - - -
28E PHE 4.5 0.9 - - - +
29E THR* 1.3 110.8 + - - +
31E ASP* 1.3 65.3 + - - +
32E TRP* 5.1 1.8 - - + -
76E SER* 3.4 7.1 - - - -
77E GLY 2.9 31.7 + - - +
78E TYR 4.2 3.9 + - - -
106E LEU* 3.6 38.5 - - + +
107E HIS 3.0 28.4 + - - -
108E LEU* 5.4 3.1 - - - -
109E GLU* 5.5 1.6 - - + -
16F PRO* 5.8 5.8 - - + -
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Residues in contact with ASP 31 (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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16E ARG 4.5 0.3 - - - -
17E ALA* 3.3 1.9 - - - -
18E GLN* 2.7 48.4 + - + +
20E ARG* 3.1 32.5 + - + +
30E HIS* 1.3 71.2 - - - +
32E TRP* 1.3 61.7 + - - +
75E GLU 3.6 3.9 - - - +
76E SER* 2.4 33.1 + - - -
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Residues in contact with TRP 32 (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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16E ARG 3.1 14.8 - - - +
17E ALA* 4.1 9.6 - - + -
30E HIS* 5.0 3.1 - - + -
31E ASP* 1.3 76.8 - - - +
33E MET* 1.3 68.1 + - - +
34E VAL* 4.0 2.7 - - + -
55E LEU* 3.7 24.7 - - + -
59E PHE* 3.6 22.0 - + - -
73E VAL* 3.7 27.1 - - + -
74E GLU* 3.8 0.9 - - - +
75E GLU* 2.9 62.5 + - + +
76E SER 4.3 0.2 - - - -
77E GLY* 4.1 24.7 - - - +
79E ALA 4.9 2.6 + - - -
81E PHE* 4.0 14.8 - + - -
104E LEU* 3.5 43.8 - - + +
106E LEU* 4.4 11.4 - - + -
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Residues in contact with MET 33 (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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15E HIS* 3.1 3.5 - - - -
16E ARG* 2.8 64.6 + - + +
32E TRP* 1.3 78.8 - - - +
34E VAL* 1.3 61.9 + - - +
35E PHE* 3.6 41.7 - - + -
72E LYS* 3.7 38.4 - - + +
73E VAL 3.4 12.8 - - - +
74E GLU* 4.2 10.1 - - + -
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Residues in contact with VAL 34 (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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14E GLY 3.2 15.9 - - - +
15E HIS* 3.7 10.1 - - + -
32E TRP* 4.0 2.1 - - + -
33E MET* 1.3 75.1 - - - +
35E PHE* 1.3 64.7 + - - +
53E PHE* 3.7 18.1 - - + -
72E LYS* 3.2 5.4 - - - +
73E VAL* 3.2 47.3 + - + -
83E LEU* 4.0 12.8 - - + -
85E ILE* 4.6 9.6 - - + -
102E TYR* 3.8 23.3 - - + -
104E LEU* 3.7 13.0 - - + -
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Residues in contact with PHE 35 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E GLU 4.2 2.9 - - - -
13E LEU* 3.3 5.2 - - - +
14E GLY* 2.8 73.6 + - - -
15E HIS* 3.8 5.8 - - - -
16E ARG* 5.7 3.6 - - + -
33E MET* 3.6 35.9 - - + -
34E VAL* 1.3 78.0 - - - +
36E VAL* 1.3 68.7 + - - +
37E ARG* 3.4 58.8 - - + -
53E PHE* 4.5 3.4 - - - -
71E TYR 3.3 10.8 - - - +
72E LYS* 4.2 2.0 - - + -
85E ILE* 5.2 0.2 - - - +
115E ASN* 5.6 5.2 - - - -
116E HIS 4.7 2.9 - - - -
117E LEU* 4.0 11.0 - - + -
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Residues in contact with VAL 36 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E LEU* 4.7 7.9 - - + -
12E GLU 3.3 7.6 - - - +
13E LEU* 3.7 26.2 - - + -
35E PHE* 1.3 80.4 - - - +
37E ARG* 1.3 66.2 + - - +
44E ILE* 4.6 10.5 - - + -
51E VAL* 4.1 13.9 - - + -
53E PHE* 4.2 4.5 - - + -
71E TYR* 2.8 43.8 + - + +
85E ILE* 3.8 26.5 - - + -
87E VAL* 4.4 16.6 - - + -
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Residues in contact with ARG 37 (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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116C HIS* 4.1 14.1 + - - -
117C LEU* 2.9 30.3 + - - +
202C CU 4.2 16.8 - - - -
11E LEU* 3.7 2.9 - - - +
12E GLU* 2.8 57.2 + - + +
35E PHE* 3.4 38.2 - - + -
36E VAL* 1.3 75.4 - - - +
38E GLY* 1.3 70.6 + - - +
44E ILE* 4.3 10.1 - - - -
71E TYR* 5.4 0.2 - - - -
117E LEU* 3.5 19.2 - - - +
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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