Contacts of the strand formed by residues 97 - 102 (chain A) in PDB entry 5UV6
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 GLN 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ARG* 2.6 41.5 + - + +
57A CYS 3.3 13.9 - - - +
58A THR* 5.1 1.8 - - - +
59A ILE* 4.4 2.8 - - - +
92A VAL* 3.6 22.3 - - + +
93A ASN* 3.6 3.1 - - - -
94A THR* 2.9 36.6 + - - +
95A PRO 3.6 0.2 - - - -
96A THR* 1.3 82.6 - - + +
98A TYR* 1.3 60.0 + - - +
99A SER* 2.6 20.5 + - - +
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Residues in contact with TYR 98 (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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57A CYS* 3.0 26.8 + - + +
59A ILE* 4.3 6.2 - - + +
66A VAL* 3.4 39.9 - - + -
67A ALA* 3.7 9.2 - - - -
68A TRP* 2.8 64.6 + + + -
76A TYR* 3.1 23.3 - - + +
78A GLY* 2.6 44.4 + - - -
90A ILE* 3.8 14.1 - - + -
92A VAL 3.3 8.1 - - - -
93A ASN* 3.8 15.5 - - - +
94A THR 5.4 0.4 - - - +
97A GLN* 1.3 74.0 - - - +
99A SER* 1.3 60.0 + - - +
100A ILE* 5.0 1.3 - - + -
115A CYS* 5.2 0.9 - - - -
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Residues in contact with SER 99 (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 LEU 3.0 11.0 - - - -
56A ARG* 3.2 25.0 - - - -
68A TRP* 3.9 0.2 - - - +
90A ILE* 4.0 1.0 - - - +
91A LEU* 2.8 33.8 + - - +
92A VAL* 2.9 23.6 + - - +
97A GLN* 2.6 38.6 + - - +
98A TYR* 1.3 72.5 - - - +
100A ILE* 1.3 59.9 + - - +
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Residues in contact with ILE 100 (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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54A THR* 3.7 2.4 - - - +
55A LEU* 2.9 43.3 + - + +
68A TRP* 3.6 42.4 - - + +
75A LEU* 3.7 26.2 - - + -
76A TYR* 4.0 29.2 - - + -
88A VAL* 4.1 11.2 - - + -
89A ILE 3.3 12.1 - - - +
90A ILE* 4.1 9.0 - - + -
91A LEU* 3.9 7.3 - - - +
98A TYR* 5.0 1.8 - - + -
99A SER* 1.3 78.4 - - - +
101A MET* 1.3 64.3 + - - +
102A ILE* 5.1 2.9 - - + -
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Residues in contact with MET 101 (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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52A SER* 3.9 22.9 - - - -
53A ALA 3.2 12.8 - - - +
54A THR* 3.4 20.0 - - - +
55A LEU* 4.8 0.4 - - - +
87A ARG 3.0 4.9 - - - +
88A VAL* 3.3 2.6 - - - -
89A ILE* 2.8 46.7 + - + +
91A LEU* 3.6 26.7 - - + -
100A ILE* 1.3 78.3 - - - +
102A ILE* 1.3 71.7 + - - +
103A GLN* 4.0 16.6 - - + +
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Residues in contact with ILE 102 (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 ALA* 2.9 34.5 + - + +
55A LEU* 4.3 12.1 - - + -
75A LEU* 4.9 2.9 - - + -
87A ARG* 3.3 33.0 - - + +
88A VAL* 4.3 15.7 - - + -
100A ILE* 5.1 2.7 - - + -
101A MET* 1.3 73.6 - - - +
103A GLN* 1.3 59.5 - - - +
105A VAL* 3.1 14.3 - - + +
109A ASP* 3.9 8.3 - - + +
113A TYR* 3.6 41.5 - - + +
130A LEU* 4.3 13.5 - - + -
1C NAG 3.6 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