Contacts of the strand formed by residues 92 - 98 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ASN* 2.9 3.9 - - - -
89A ILE* 2.8 42.7 + - + +
90A ASN* 3.2 10.7 - - + +
91A GLY* 1.3 78.9 - - - +
93A THR* 1.3 65.4 + - - +
94A CYS 3.4 0.3 + - - -
115A SER* 4.2 26.5 - - - +
117A ASP* 4.9 13.6 + - + +
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Residues in contact with THR 93 (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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87A ASP* 3.5 18.6 - - + +
88A ASN* 4.2 1.7 - - - +
91A GLY 3.9 3.1 + - - -
92A LYS* 1.3 72.7 - - - +
94A CYS* 1.3 73.4 + - - +
95A THR* 4.5 6.9 - - + +
115A SER* 3.6 15.1 - - - -
116A ALA* 4.1 6.4 + - - +
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Residues in contact with CYS 94 (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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86A PRO* 4.8 1.1 - - - -
87A ASP* 3.4 7.6 + - - +
88A ASN* 3.7 18.6 - - - -
89A ILE* 3.7 22.7 - - - -
93A THR* 1.3 81.8 - - - +
95A THR* 1.3 67.8 + - - +
113A TRP* 3.4 41.2 - - + +
114A GLU 3.7 11.7 - - - +
115A SER 4.3 0.2 - - - +
151B VAL* 3.4 29.8 - - - -
14O G 5.3 1.6 - - - +
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Residues in contact with THR 95 (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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93A THR* 4.5 9.9 - - + +
94A CYS* 1.3 80.3 - - - +
96A ALA* 1.3 65.0 + - - +
97A SER 4.7 0.2 + - - -
112A CYS 3.4 0.3 - - - +
113A TRP* 3.0 20.2 - - - -
114A GLU 3.0 31.1 + - - +
115A SER 4.5 3.1 + - - -
116A ALA* 4.8 12.8 - - + +
119A ASN* 4.1 7.6 + - - +
13O G 3.1 29.3 - - + +
14O G 3.7 21.8 - - - -
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Residues in contact with ALA 96 (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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78A HIS* 3.7 38.8 - - + +
82A PHE* 4.5 4.0 - - + -
95A THR* 1.3 77.1 - - - +
97A SER* 1.3 53.9 - - - +
98A HIS* 5.5 0.4 - - + -
111A LEU* 4.7 6.3 - - + -
112A CYS 3.3 6.7 - - - +
113A TRP* 3.9 7.4 - - + -
13O G 2.6 39.4 + - - +
14O G 3.3 16.0 + - - +
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Residues in contact with SER 97 (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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95A THR 3.8 0.4 + - - -
96A ALA* 1.3 72.8 - - - +
98A HIS* 1.3 66.4 + - - +
99A LEU 3.5 2.6 + - - -
111A LEU* 3.5 7.0 - - - -
112A CYS* 2.7 40.5 + - - +
114A GLU* 2.4 37.1 + - - +
119A ASN* 2.8 30.7 - - - +
122A ARG* 4.6 3.1 - - - -
13O G 3.6 4.5 - - - -
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Residues in contact with HIS 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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78A HIS* 2.9 31.6 + + - -
96A ALA 5.5 0.4 - - - -
97A SER* 1.3 73.6 - - - +
99A LEU* 1.3 64.2 + - - +
100A CYS* 3.2 4.3 - - - +
101A HIS* 3.7 38.6 + - - +
102A ASN 3.0 21.7 + - - +
103A THR* 3.1 35.9 + - + +
105A CYS* 3.4 6.2 + - - -
110A HIS 3.8 4.7 - - - +
111A LEU* 2.9 31.0 - - + -
119A ASN* 5.1 1.6 - - - +
122A ARG* 4.9 2.4 - - - -
13O G 3.2 32.1 + - - +
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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