Contacts of the strand formed by residues 30 - 37 (chain A) in PDB entry 5J9S
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLN 3.2 15.9 - - - +
19A LEU* 3.5 25.3 - - + +
20A ARG* 4.4 1.1 - - - -
28A PHE* 3.6 0.7 - - - +
29A THR* 1.3 102.3 + - - +
31A ASP* 1.3 66.4 + - - +
32A TRP* 4.1 2.5 + - + -
76A SER* 3.2 6.4 - - - -
77A GLY 2.9 29.9 + - - +
78A TYR 5.4 1.3 - - - -
106A LEU* 3.5 48.9 - - + +
107A ASN* 2.8 47.0 + - - -
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Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ARG 4.2 0.2 - - - +
17A ALA* 3.5 1.2 - - - +
18A GLN* 2.9 42.6 + - + +
20A ARG* 3.0 43.2 + - - +
24A THR* 5.3 0.3 - - - +
30A HIS* 1.3 71.7 - - - +
32A TRP* 1.3 61.5 + - - +
75A GLU 3.5 5.2 - - - +
76A SER* 2.2 28.1 + - - -
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Residues in contact with TRP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A HIS* 5.0 0.9 - - + -
16A ARG 3.1 13.7 - - - +
17A ALA* 4.1 11.4 - - + -
30A HIS* 4.5 9.9 - - + -
31A ASP* 1.3 76.6 - - - +
33A MET* 1.3 67.5 + - - +
34A VAL* 3.8 17.0 - - + -
55A LEU* 4.0 23.1 - - + -
59A PHE* 3.7 22.0 - + - -
73A VAL* 3.9 9.2 - - + -
74A GLU* 3.4 2.9 - - - +
75A GLU* 2.8 64.8 + - + +
76A SER 4.3 1.4 - - - -
77A GLY* 4.2 14.4 - - - +
79A ALA 5.2 3.6 + - - -
81A PHE* 4.0 9.9 - + - -
83A MET* 4.0 5.2 - - + -
104A LEU* 3.4 35.0 - - + +
106A LEU* 3.8 22.2 - - + -
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Residues in contact with MET 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A HIS* 3.0 4.9 - - - -
16A ARG* 2.8 65.9 + - + +
32A TRP* 1.3 76.6 - - - +
34A VAL* 1.3 61.9 - - - +
35A PHE* 3.6 33.9 - - + -
72A LYS* 3.9 20.2 - - + +
73A VAL 3.2 7.2 - - - +
74A GLU* 3.6 30.7 - - + +
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLY 3.4 13.5 - - - +
15A HIS* 3.8 6.1 - - + -
32A TRP* 3.8 11.3 - - + -
33A MET* 1.3 73.7 - - - +
35A PHE* 1.3 66.1 + - - +
53A PHE* 3.9 12.2 - - + -
72A LYS* 3.1 3.8 - - - +
73A VAL* 2.8 42.1 + - + +
83A MET* 3.7 36.8 - - + -
85A ILE* 4.2 15.9 - - + -
102A TYR* 4.3 11.2 - - + -
104A LEU* 3.8 12.8 - - + -
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLU 4.9 0.4 - - - -
13A LEU* 3.8 2.5 - - - +
14A GLY* 2.9 62.4 + - - +
15A HIS* 3.5 8.7 - - - -
16A ARG* 5.3 5.4 - - - -
33A MET* 3.6 26.0 - - + -
34A VAL* 1.3 77.4 - - - +
36A VAL* 1.3 73.2 + - - +
37A ARG* 3.6 49.4 - - + -
53A PHE* 4.2 2.5 - - - -
71A TYR 3.2 11.4 - - - +
72A LYS* 3.7 10.3 - - + +
85A ILE* 5.4 0.7 - - - +
115A ASN* 5.6 3.4 - - - -
116A HIS 4.6 2.0 - - - -
117A LEU* 3.7 19.3 - - + -
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.2 12.1 - - + -
12A GLU 3.4 11.0 - - - +
13A LEU* 4.4 13.9 - - + -
35A PHE* 1.3 80.2 - - - +
37A ARG* 1.3 66.7 + - - +
44A ILE* 4.1 17.0 - - + -
51A VAL* 3.9 13.2 - - + -
53A PHE* 3.8 18.4 - - + -
71A TYR* 2.8 38.4 + - + +
85A ILE* 3.9 21.1 - - + -
87A VAL* 4.3 15.5 - - + -
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.7 4.5 - - - +
12A GLU* 2.5 67.4 + - + +
35A PHE* 3.6 29.9 - - + -
36A VAL* 1.3 76.4 - - - +
38A GLY* 1.3 66.2 + - - +
44A ILE* 4.1 13.0 - - - -
71A TYR* 5.4 0.7 - - - -
117A LEU* 3.5 22.0 - - - +
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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