Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 3ZVU
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 THR 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 3.6 5.5 - - - -
67A VAL* 4.1 15.8 - - - +
68A GLU 5.1 1.6 + - - -
71A PHE* 4.6 3.8 - - - -
76A GLY 3.7 9.4 - - - +
77A CYS* 1.3 81.2 - - - +
79A ARG* 1.3 63.9 + - - +
80A ASP* 5.2 1.9 + - - -
93A THR* 4.7 10.3 - - + +
94A GLU 3.1 13.7 - - - +
95A ARG* 4.1 7.4 - - + -
111A ILE* 4.0 22.2 - - + -
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG 4.7 0.4 + - - -
52A PHE* 2.9 63.3 + - + +
55A PRO* 3.7 21.3 - - - +
59A LYS* 3.7 11.5 - - - +
65A CYS* 3.8 25.1 - - - -
66A SER 3.6 7.2 - - - +
67A VAL* 4.1 7.4 - - + -
78A THR* 1.3 73.7 - - - +
80A ASP* 1.3 65.5 - - - +
81A VAL* 4.2 4.2 - - + +
92A SER 3.7 0.7 - - - +
93A THR* 3.5 2.4 - - - +
94A GLU* 2.6 62.0 + - + +
108A PHE* 3.6 32.5 - - - -
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER 4.0 0.2 - - - +
65A CYS* 3.4 3.2 - - - -
66A SER* 2.9 46.3 + - - +
78A THR* 5.2 2.2 + - - -
79A ARG* 1.3 71.2 - - - +
81A VAL* 1.3 63.7 + - - +
82A ILE* 4.0 5.6 + - + +
92A SER 3.5 3.6 - - - +
93A THR* 3.3 28.9 + - - +
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Residues in contact with VAL 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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55A PRO* 4.5 0.4 - - + -
62A ILE* 3.7 39.7 - - + -
64A SER 3.6 2.7 - - - -
65A CYS* 3.9 22.2 - - + -
79A ARG* 4.2 8.1 - - + +
80A ASP* 1.3 74.8 - - - +
82A ILE* 1.3 72.2 + - - +
83A VAL* 4.2 10.8 - - + -
91A THR* 3.2 7.4 - - - +
92A SER* 2.6 49.7 + - - +
94A GLU* 3.9 23.8 - - - +
192A A8S 5.1 2.2 - - - +
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Residues in contact with ILE 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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62A ILE* 3.8 1.7 - - - +
63A LYS* 2.8 42.5 + - - +
64A SER* 2.8 33.8 + - - +
80A ASP* 5.0 5.2 - - + +
81A VAL* 1.3 80.0 - - - +
83A VAL* 1.3 69.4 + - - +
90A ASN* 3.6 11.7 - - + +
91A THR* 4.3 13.7 - - + -
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Residues in contact with VAL 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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61A PHE 3.3 16.4 - - - +
62A ILE* 4.7 0.9 - - + -
63A LYS* 3.8 8.8 - - - +
81A VAL* 4.2 12.3 - - + +
82A ILE* 1.3 87.3 - - - +
84A ILE* 1.3 68.3 + - - +
87A LEU* 3.6 19.7 - - + -
89A ALA* 3.5 31.0 - - + +
90A ASN* 3.2 19.2 + - - +
91A THR 4.4 0.2 - - - +
192A A8S 3.7 36.1 - - + +
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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