Contacts of the strand formed by residues 95 - 101 (chain A) in PDB entry 2W93
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ALA 5.1 1.8 - - - +
58A ALA* 3.9 7.0 - - + +
59A ASP* 4.0 17.5 - - - +
68A SER* 3.5 20.9 - - - +
70A ILE* 3.7 28.7 - - + +
85A ILE* 4.1 13.2 - - + -
88A SER* 3.6 30.3 - - - +
93A VAL* 3.1 10.0 + - + +
94A GLY* 1.3 73.3 - - - -
96A LEU* 1.3 62.9 + - - +
97A HIS 3.6 1.0 + - - -
156A THR* 3.5 3.7 - - - +
162A PRO* 3.0 27.6 - - + +
163A VAL 3.1 3.6 + - - -
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Residues in contact with LEU 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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10A LEU* 4.5 7.9 - - + -
14A LEU* 4.4 10.1 - - + -
67A MET* 4.4 6.1 - - + -
68A SER 2.9 18.5 + - - +
69A CYS* 3.2 11.6 - - - -
70A ILE 2.9 25.8 + - - +
95A VAL* 1.3 71.0 - - - +
97A HIS* 1.3 59.5 + - - +
98A VAL* 3.7 20.9 + - + -
152A CYS* 3.9 24.5 - - + +
153A ILE* 4.0 24.5 - - + -
156A THR* 3.7 20.9 - - - +
163A VAL* 3.7 14.8 - - + +
165A LEU* 4.3 14.8 - - + -
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Residues in contact with HIS 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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70A ILE* 3.4 19.1 - - + -
72A THR* 2.8 33.4 + - + +
78A GLU* 3.7 29.6 - - + -
81A ALA* 4.1 9.8 - - + +
82A LEU* 4.4 7.7 - - + +
85A ILE* 3.8 31.7 - - + +
95A VAL 3.6 2.1 + - - +
96A LEU* 1.3 70.1 - - - +
98A VAL* 1.3 71.4 + - - +
99A VAL* 3.6 8.4 + - + +
129A SER* 4.7 0.4 + - - -
162A PRO* 5.9 0.2 - - + -
163A VAL 2.9 14.9 + - - +
164A TYR* 3.4 16.3 - + + +
165A LEU 2.8 25.6 + - - -
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Residues in contact with VAL 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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10A LEU* 4.4 8.5 - - + -
33A LEU* 4.1 16.8 - - + -
69A CYS* 4.0 11.9 - - - -
70A ILE 2.8 9.8 + - - +
71A ILE* 3.1 12.5 - - + +
72A THR 2.9 23.9 + - - -
96A LEU* 3.9 27.8 - - + -
97A HIS* 1.3 77.8 - - - +
99A VAL* 1.3 66.5 + - - +
100A GLY 4.2 0.2 - - - -
165A LEU* 3.2 24.0 - - + +
167A LEU* 3.8 28.3 - - + -
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Residues in contact with VAL 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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72A THR* 3.5 6.5 - - - +
73A THR 3.9 4.0 - - - -
74A PHE* 3.7 20.0 - - - +
78A GLU* 3.6 28.0 - - + +
97A HIS* 3.6 22.0 - - + +
98A VAL* 1.3 81.6 - - - +
100A GLY* 1.3 65.3 + - - +
101A VAL* 3.5 9.2 - - + +
164A TYR* 3.5 37.2 - - + +
165A LEU 2.9 8.2 + - - +
166A GLY* 3.4 1.8 - - - -
167A LEU* 2.8 26.3 + - - +
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Residues in contact with GLY 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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29A PHE* 3.3 27.7 - - - +
30A ASN* 4.1 11.2 - - - +
33A LEU* 5.5 3.6 - - - -
71A ILE* 4.9 2.2 - - - +
72A THR 3.0 13.3 + - - -
73A THR 3.9 0.2 - - - -
74A PHE* 3.0 25.8 + - - +
98A VAL* 4.2 0.6 - - - +
99A VAL* 1.3 70.0 - - - +
101A VAL* 1.3 60.1 + - - -
167A LEU* 3.5 9.0 - - - -
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Residues in contact with VAL 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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29A PHE* 4.2 5.1 - - - +
74A PHE* 3.9 17.0 - - + -
99A VAL* 3.5 22.7 - - + +
100A GLY* 1.3 79.2 - - - +
102A PRO* 1.3 80.1 - - + +
107A GLN* 3.8 9.2 - - - +
138A MET* 4.0 20.0 - - + -
164A TYR* 4.8 2.0 - - - +
166A GLY* 4.3 9.2 - - - -
167A LEU 3.1 7.6 + - - -
168A PRO* 3.5 33.2 - - + -
169A ALA* 3.0 23.0 + - - +
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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