Contacts of the strand formed by residues 70 - 76 (chain A) in PDB entry 2J3W
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 TRP 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A SER* 3.5 30.1 - - - -
5A PHE* 4.2 2.0 - - - -
6A TYR* 4.6 3.4 - - + -
23A LEU* 4.2 11.2 - - + -
34A HIS* 6.3 0.6 - - - -
37A LEU* 6.2 0.6 - - + +
38A ASN* 2.6 35.9 + - - -
41A ILE* 3.6 26.0 - - + -
66A LYS* 3.3 4.1 - - - -
67A PHE* 2.9 40.8 + - + +
68A ASN* 3.2 2.6 - - + -
69A GLU* 1.3 75.9 - - + +
71A PHE* 1.3 64.8 + - - +
72A VAL* 3.6 1.7 + - - +
86A LEU* 3.5 25.7 - - + +
87A HIS* 3.2 42.4 - - - -
88A ASP* 3.1 30.1 - - - -
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Residues in contact with PHE 71 (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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63A THR* 4.8 6.1 - - + -
65A ASP 3.8 5.6 - - - -
66A LYS* 3.5 42.6 - - + -
69A GLU 3.5 4.6 + - - -
70A TRP* 1.3 73.1 - - - +
72A VAL* 1.3 60.0 + - - +
86A LEU* 3.5 4.0 - - - -
87A HIS* 2.7 64.9 + - + +
88A ASP 3.7 22.0 - - - -
89A VAL* 4.9 0.2 - - - -
90A ARG* 3.0 61.5 - - + -
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Residues in contact with VAL 72 (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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41A ILE* 4.5 11.9 - - + -
45A ALA* 3.6 28.3 - - + -
63A THR* 3.2 3.0 - - - -
64A VAL* 2.6 42.9 + - + +
65A ASP* 2.8 33.1 + - + +
66A LYS* 4.5 2.0 - - - +
67A PHE* 4.5 2.2 - - + +
70A TRP 3.9 9.6 - - - +
71A PHE* 1.3 76.9 - - - +
73A SER* 1.3 66.0 + - - +
84A ILE* 4.3 6.1 - - + -
85A MET 3.6 1.6 - - - -
86A LEU* 3.7 24.5 - - + -
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Residues in contact with SER 73 (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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60A TYR* 4.7 3.3 + - - -
62A LYS* 3.1 13.3 + - - -
63A THR* 3.6 14.9 - - - +
72A VAL* 1.3 77.7 - - - +
74A ALA* 1.3 64.7 + - - +
84A ILE* 3.7 2.6 - - - -
85A MET* 2.9 34.3 + - - -
87A HIS* 2.8 29.6 + - - -
95A ILE* 4.2 21.8 - - - +
99A PHE* 4.4 3.1 - - - -
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Residues in contact with ALA 74 (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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49A VAL* 3.6 32.5 - - + -
60A TYR* 3.6 8.1 - - - -
61A LEU* 2.8 44.8 + - + -
62A LYS 3.1 7.1 + - - -
64A VAL* 4.5 6.7 - - + -
73A SER* 1.3 78.9 - - - +
75A PHE* 1.3 57.3 + - - +
83A PHE 3.2 11.0 - - - +
84A ILE* 4.2 2.0 - - + -
99A PHE* 3.8 4.0 - - - -
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Residues in contact with PHE 75 (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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59A MET* 3.1 47.6 - - + -
60A TYR* 3.6 27.1 - + + -
74A ALA* 1.3 74.4 - - - +
76A VAL* 1.3 63.7 + - - +
77A THR* 4.1 8.3 - - + -
81A MET 3.6 1.7 - - - +
82A ARG* 3.7 1.9 - - - -
83A PHE* 2.7 60.2 + + + +
96A LYS* 5.3 2.5 - - + -
99A PHE* 3.5 33.9 - + + -
100A THR* 4.2 17.7 - - - -
103A TYR* 3.9 31.4 - + + -
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Residues in contact with VAL 76 (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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49A VAL* 3.9 18.6 - - + -
53A MET* 4.1 23.6 - - + -
59A MET* 2.7 37.7 + - - +
61A LEU* 3.8 25.8 - - + -
75A PHE* 1.3 76.2 - - - +
77A THR* 1.3 63.7 + - - +
80A HIS* 4.1 16.4 - - + -
81A MET 3.5 4.9 - - - +
82A ARG* 4.4 5.2 - - + -
78B ARG* 3.2 34.8 - - - +
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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