Contacts of the strand formed by residues 92 - 98 (chain B) in PDB entry 1EVW
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 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B ASN* 3.0 3.2 - - - -
89B ILE* 2.8 44.1 + - + +
90B ASN* 3.1 12.0 - - + +
91B GLY* 1.3 79.5 - - - +
93B THR* 1.3 66.0 + - - +
94B CYS 3.4 0.3 + - - -
115B SER* 4.2 26.0 - - - +
117B ASP* 4.8 13.3 + - + +
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Residues in contact with THR 93 (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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87B ASP* 3.4 14.7 + - + +
88B ASN* 4.2 2.1 - - - +
91B GLY 3.8 4.2 + - - -
92B LYS* 1.3 72.7 - - - +
94B CYS* 1.3 73.2 + - - +
95B THR* 4.4 9.3 - - + +
115B SER* 3.7 15.2 - - - -
116B ALA* 4.1 6.2 + - - +
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Residues in contact with CYS 94 (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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151A VAL* 3.3 30.1 - - + -
86B PRO 4.7 0.9 - - - -
87B ASP* 3.3 7.1 + - - +
88B ASN* 3.5 23.1 - - - -
89B ILE* 3.7 9.0 - - - -
92B LYS 3.7 9.2 - - - -
93B THR* 1.3 79.8 - - - +
95B THR* 1.3 69.5 + - - +
113B TRP* 3.5 40.1 - - + +
114B GLU 3.7 11.2 - - - +
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Residues in contact with THR 95 (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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93B THR* 4.4 14.1 - - + +
94B CYS* 1.3 80.4 - - - +
96B ALA* 1.3 60.9 + - - +
112B CYS 3.2 0.7 - - - +
113B TRP* 2.9 20.0 - - - -
114B GLU 3.0 31.5 + - - +
115B SER 4.5 2.6 + - - -
116B ALA* 4.9 12.8 - - + +
119B ASN* 4.0 5.7 + - - +
14M G 3.0 37.8 - - + +
15M A 3.5 15.7 - - - +
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Residues in contact with ALA 96 (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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78B HIS* 3.4 39.3 - - + +
82B PHE* 4.6 4.5 - - + -
95B THR* 1.3 72.8 - - - +
97B SER* 1.3 52.8 + - - +
98B HIS* 4.9 1.6 + - - -
111B LEU* 4.8 5.6 - - + -
112B CYS 3.2 6.1 - - - +
113B TRP* 3.9 6.3 - - + -
14M G 2.5 49.6 + - - +
15M A 2.9 13.3 + - - +
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Residues in contact with SER 97 (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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95B THR* 3.8 0.4 + - - -
96B ALA* 1.3 69.5 - - - +
98B HIS* 1.3 63.2 + - - +
99B LEU 3.5 0.7 + - - -
111B LEU* 3.3 8.3 - - - -
112B CYS* 2.7 42.4 + - - +
114B GLU* 2.9 34.0 + - - -
119B ASN* 3.1 26.0 + - - +
122B ARG* 3.9 6.1 - - - -
604B MG 3.3 5.7 - - - -
14M G 2.7 6.3 - - - -
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Residues in contact with HIS 98 (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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61B ARG* 5.9 2.5 - - - -
78B HIS* 2.9 45.7 + + + -
96B ALA 5.4 1.3 - - - -
97B SER* 1.3 68.5 + - - +
99B LEU* 1.3 61.4 + - - +
100B CYS* 3.2 12.1 - - - +
101B HIS* 3.6 28.5 + - - +
102B ASN 2.9 27.2 + - - -
103B THR* 3.7 16.4 + - + -
105B CYS* 3.2 5.5 + - + -
110B HIS 3.7 2.9 - - - -
111B LEU* 3.7 13.7 - - + -
122B ARG* 4.9 1.0 - - - -
604B MG 3.0 19.3 - - - -
14M G 2.4 50.6 + - - +
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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