Contacts of the strand formed by residues 80 - 85 (chain A) in PDB entry 3JWE
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 LEU 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP 3.7 3.3 - - - +
47A PRO* 3.8 6.9 - - - +
52A LYS* 5.3 2.0 - - + -
53A ALA* 3.5 34.1 - - + +
54A LEU 4.7 0.4 - - - -
55A ILE* 4.1 28.7 - - + -
75A LEU* 3.3 17.0 + - + +
76A MET* 3.4 20.3 + - - -
78A LEU* 3.7 35.0 - - + +
79A ASP* 1.3 79.8 - - - +
81A LEU* 1.3 60.2 + - - +
82A VAL* 3.5 2.8 + - - +
127A PHE* 4.7 2.2 - - + -
300A VAL* 3.7 33.2 - - + -
301A SER* 5.9 0.9 - - - +
304A THR* 4.8 9.2 - - + +
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Residues in contact with LEU 81 (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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44A TYR* 4.7 2.5 - - + -
45A TRP 3.9 2.7 - - - -
46A LYS* 4.1 33.2 - - + -
47A PRO* 4.1 3.8 - - + -
51A PRO* 4.1 15.7 - - + +
53A ALA 3.0 9.3 + - - +
54A LEU* 3.5 16.0 - - + -
55A ILE* 3.1 25.4 + - - +
80A LEU* 1.3 69.5 - - - +
82A VAL* 1.3 76.8 + - - +
83A PHE* 3.9 5.9 + - + -
117A MET* 3.7 22.4 - - + -
121A TYR* 3.4 48.5 - - + +
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Residues in contact with VAL 82 (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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44A TYR* 3.4 3.1 - - - -
45A TRP* 2.9 58.6 + - + +
55A ILE* 3.6 15.5 - - + +
57A VAL* 3.8 28.0 - - + -
72A ALA* 3.6 30.1 - - + +
75A LEU* 3.7 20.6 - - + -
76A MET 4.0 1.1 - - - +
80A LEU 3.9 9.4 - - - +
81A LEU* 1.3 78.7 - - - +
83A PHE* 1.3 62.9 + - - +
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Residues in contact with PHE 83 (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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43A ARG 3.4 5.4 - - - -
44A TYR* 3.6 22.7 - - + -
45A TRP* 4.5 2.2 - - - -
54A LEU* 4.1 19.3 - - + -
55A ILE 3.1 30.1 + - - -
56A PHE* 3.3 29.1 - + + -
57A VAL* 3.0 24.1 + - - +
81A LEU* 4.1 10.5 - - + -
82A VAL* 1.3 75.7 - - - +
84A ALA* 1.3 60.7 + - - +
113A HIS* 3.8 30.7 - + - -
114A VAL* 3.8 26.0 - - + -
117A MET* 3.6 34.8 - - + -
126A VAL* 4.7 4.9 - - + -
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Residues in contact with ALA 84 (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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42A CYS* 3.4 0.3 - - - -
43A ARG* 3.0 28.9 + - + +
45A TRP* 4.1 14.6 - - + -
56A PHE* 3.9 8.7 - - - -
57A VAL* 3.5 23.1 - - + +
65A SER* 3.8 21.5 - - - -
83A PHE* 1.3 75.5 - - - +
85A HIS* 1.3 61.3 + - - +
113A HIS* 3.2 18.0 - - - -
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Residues in contact with HIS 85 (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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32A LEU* 3.8 5.1 - - + +
40A LEU* 4.0 19.3 - - + +
41A PHE 3.1 15.3 - - - +
42A CYS* 4.1 7.2 - - - +
56A PHE* 3.7 22.7 - + - -
57A VAL 4.7 3.1 - - - +
59A HIS* 3.8 12.0 - - - -
65A SER* 4.4 4.2 - - - -
84A ALA* 1.3 76.6 - - - +
86A ASP* 1.3 79.9 + - - +
87A HIS* 3.5 22.6 + - - -
109A ASP* 3.3 38.7 - - + +
110A VAL* 3.8 3.8 - - - +
113A HIS* 2.9 28.6 + - + +
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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