Contacts of the strand formed by residues 77 - 86 (chain A) in PDB entry 6OZE
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 VAL 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A VAL* 4.9 2.9 - - + -
69A VAL 3.6 5.6 - - - +
70A LEU* 3.9 12.8 - - + -
75A LEU 5.4 0.4 - - - +
76A GLU* 1.3 74.9 + - - +
78A VAL* 1.3 63.8 + - - +
79A TYR* 3.6 25.1 - - - +
80A GLU* 3.7 24.9 - - + +
238A GLN* 3.9 38.1 - - + +
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Residues in contact with VAL 78 (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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47A ARG* 4.9 4.7 - - + -
69A VAL* 2.8 37.3 + - + +
70A LEU 4.4 0.4 - - - -
71A SER* 4.3 19.3 - - - +
76A GLU* 3.8 11.4 - - + +
77A VAL* 1.3 77.7 - - - +
79A TYR* 1.3 60.5 + - - +
118A LEU* 3.7 33.0 - - + +
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Residues in contact with TYR 79 (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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67A LEU* 4.1 20.0 - - + -
68A VAL* 3.2 3.3 - - - -
69A VAL* 2.9 43.6 + - + -
77A VAL* 3.6 7.4 - - - +
78A VAL* 1.3 79.1 - - - +
80A GLU* 1.3 69.3 + - - +
81A GLU* 3.6 29.9 - - + +
107A LEU 4.9 1.3 + - - -
110A GLN* 4.0 7.1 + - - -
111A LEU* 3.5 41.4 + - + +
114A LYS* 2.6 40.8 + - - -
115A GLU* 5.3 2.0 - - + -
118A LEU* 4.2 17.9 - - + -
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Residues in contact with GLU 80 (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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67A LEU 3.4 6.5 - - - -
68A VAL* 4.0 14.1 - - + -
77A VAL* 3.7 19.3 - - + +
79A TYR* 1.3 85.8 - - - +
81A GLU* 1.3 68.8 + - - +
238A GLN* 5.7 0.7 - - - +
242A CYS* 3.7 21.6 - - - -
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Residues in contact with GLU 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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65A ALA 4.0 0.2 - - - +
66A SER* 3.2 3.7 - - - -
67A LEU* 2.9 34.7 + - + +
68A VAL* 5.2 0.4 - - - +
79A TYR* 3.6 20.2 - - + +
80A GLU* 1.3 80.3 - - - +
82A SER* 1.3 74.5 + - - +
83A ARG* 2.9 33.2 + - - +
107A LEU* 3.9 14.6 - - + +
110A GLN* 3.6 15.9 + - - +
114A LYS* 4.2 8.8 + - - -
242A CYS* 5.7 0.6 - - - -
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Residues in contact with SER 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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64A CYS* 3.8 1.6 - - - -
65A ALA 3.3 5.8 - - - -
66A SER* 2.8 21.0 + - - -
81A GLU* 1.3 82.2 - - - +
83A ARG* 1.3 69.8 + - - +
242A CYS* 3.5 22.5 + - - +
246A HIS* 3.6 42.4 + - - -
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Residues in contact with ARG 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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64A CYS* 3.4 4.9 - - - -
65A ALA* 2.9 34.2 + - + +
81A GLU* 2.9 26.6 + - - +
82A SER* 1.3 81.6 - - - +
84A MET* 1.3 68.2 + - - +
85A VAL* 3.6 11.6 + - + +
106A GLU* 4.7 15.8 + - - +
107A LEU* 3.9 19.7 - - + +
110A GLN* 2.7 45.7 + - - +
246A HIS* 4.0 2.9 - - - -
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Residues in contact with MET 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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56A VAL* 3.8 27.1 - - + -
62A ARG* 3.4 22.9 + - + +
63A ALA 3.3 17.5 - - - +
64A CYS* 4.0 2.7 - - - -
83A ARG* 1.3 75.3 - - - +
85A VAL* 1.3 63.5 + - - +
246A HIS* 3.8 21.8 + - + +
247A ILE* 3.9 22.7 - - + -
250A SER* 3.7 23.3 - - - +
251A LEU* 4.7 7.4 - - + -
301A ACT 3.3 29.6 - - - +
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Residues in contact with VAL 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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53A VAL* 5.4 1.1 - - + -
61A VAL 3.7 0.2 - - - +
62A ARG* 3.2 14.2 - - - +
63A ALA* 2.8 45.6 + - + +
65A ALA* 4.4 11.7 - - + +
83A ARG* 3.7 18.6 - - + +
84A MET* 1.3 80.3 - - - +
86A SER* 1.3 59.3 + - - +
87A LEU* 3.6 24.0 - - + -
103A PHE* 3.5 40.4 - - + -
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Residues in contact with SER 86 (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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61A VAL* 3.5 12.1 - - - +
62A ARG* 2.8 30.3 + - - +
85A VAL* 1.3 71.8 - - - +
87A LEU* 1.3 61.1 + - - +
88A THR* 3.2 25.9 + - - +
103A PHE* 3.4 17.0 - - - -
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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