Contacts of the strand formed by residues 62 - 69 (chain B) in PDB entry 3OEH
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 LYS 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B LEU* 3.9 29.6 - - + -
55B VAL 3.2 14.4 - - - +
56B GLU* 4.5 20.3 + - + -
57B PHE* 4.4 3.9 - - - -
60B GLY 3.6 13.9 + - - +
61B VAL* 1.3 84.1 - - - +
63B GLY* 1.3 59.4 + - - +
77B LEU* 3.9 1.6 - - - -
78B PHE* 2.8 31.1 + - - +
93B THR* 6.0 0.7 - - - +
113B LEU* 4.7 19.3 - - + +
115B ASN* 4.9 15.3 + - - +
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Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LEU* 3.2 11.4 - - - +
55B VAL* 3.0 32.9 + - - +
57B PHE* 4.3 1.6 - - - -
62B LYS* 1.3 76.6 - - - +
64B MET* 1.3 60.3 + - - -
75B ILE* 3.8 14.8 - - - -
76B VAL 3.2 14.4 - - - -
77B LEU* 4.4 0.2 - - - -
78B PHE* 3.8 7.2 - - - -
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Residues in contact with MET 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLU* 4.0 26.0 - - + -
53B GLU 3.5 3.1 - - - -
63B GLY* 1.3 74.4 - - - +
65B ALA* 1.3 62.8 + - - +
66B LEU* 3.1 50.8 + - + -
75B ILE* 3.2 6.9 - - - +
76B VAL* 3.0 42.3 + - + +
78B PHE* 4.0 19.3 - - + -
97B VAL* 3.4 27.8 - - + -
246B TYR* 5.5 16.4 - - + +
247B LEU* 6.4 0.9 - - - -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 3.9 18.4 - - + -
50B GLN 3.7 20.0 - - - +
51B ALA* 4.0 0.9 - - - -
52B GLU* 2.9 30.5 + - - +
53B GLU 2.9 16.7 + - - +
64B MET* 1.3 73.1 - - - +
66B LEU* 1.3 62.6 + - - +
67B ASN 3.8 0.2 - - - -
68B LEU* 4.1 7.6 - - + +
73B VAL* 4.0 14.6 - - + -
74B GLY 3.7 5.4 - - - -
75B ILE* 3.9 4.9 - - + +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ALA* 5.4 4.0 - - - +
52B GLU* 5.3 6.2 + - + +
64B MET* 3.1 27.5 + - + -
65B ALA* 1.3 75.2 - - - +
67B ASN* 1.3 64.6 + - + +
68B LEU* 4.1 4.1 + - - +
74B GLY 2.9 12.6 + - - +
76B VAL* 3.7 22.0 - - + -
283B LEU* 5.1 2.2 - - + -
287B LEU* 3.7 38.6 - - + -
289B ARG* 4.3 15.9 - - - +
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Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 5.2 4.2 - - - +
66B LEU* 1.3 88.1 - - + +
68B LEU* 1.3 60.7 + - - +
69B GLU* 2.8 31.0 + - + +
72B GLN* 5.4 1.4 + - - -
73B VAL* 3.6 2.6 - - - +
74B GLY* 2.7 52.2 + - - +
287B LEU* 4.8 16.8 - - - +
289B ARG* 5.3 8.8 - - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 3.6 33.4 - - + +
50B GLN 4.1 2.2 - - - -
51B ALA* 3.6 39.5 - - + +
65B ALA* 4.1 10.1 - - + -
66B LEU 4.1 3.3 + - - +
67B ASN* 1.3 71.4 - - - +
69B GLU* 1.3 63.3 + - - +
70B PRO* 4.7 1.4 - - - +
72B GLN 4.5 1.1 - - - -
73B VAL* 3.6 22.7 - - + +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ASN* 2.8 27.3 - - + +
68B LEU* 1.3 79.7 - - - +
70B PRO* 1.4 80.3 - - + +
71B GLY 3.3 2.6 + - - -
72B GLN* 3.0 51.4 + - - +
73B VAL* 5.6 0.9 - - - +
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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