Contacts of the strand formed by residues 95 - 102 (chain A) in PDB entry 2VR2
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLY 3.3 10.8 - - - +
65A ASP* 3.9 10.8 - - + +
90A ALA* 2.9 43.9 + - + +
91A LEU* 3.4 8.9 + - - +
93A GLY 5.0 0.7 - - - -
94A GLY* 1.3 78.4 - - - +
96A THR* 1.3 61.8 + - - +
97A MET 3.3 27.1 - - - +
98A ILE* 4.5 0.9 - - + -
127A CYS* 4.5 0.3 - - - -
352A VAL* 3.8 12.1 + - + +
355A ARG* 3.1 29.1 + - - +
356A MET* 3.8 8.8 - - - +
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Residues in contact with THR 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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62A GLY* 3.2 31.6 - - - -
63A GLY 3.0 3.7 + - - -
64A ILE* 5.8 0.3 - - - +
91A LEU* 4.0 11.0 - - + -
94A GLY 3.8 1.9 + - - +
95A THR* 1.3 73.7 - - - +
97A MET* 1.3 61.7 + - - +
127A CYS* 3.2 20.0 - - - +
128A ASP* 3.5 8.0 + - - -
402A ASP* 3.2 28.5 + - + +
403A ILE 4.6 0.7 - - - +
404A VAL* 4.7 0.7 - - + -
440A THR* 3.7 23.6 - - + -
441A ILE 3.7 24.0 - - - +
442A SER* 4.6 3.9 + - - -
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Residues in contact with MET 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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63A GLY 3.2 6.6 + - - +
64A ILE* 3.6 21.2 - - + -
65A ASP 3.0 25.6 + - - -
95A THR* 3.3 8.1 - - - +
96A THR* 1.3 82.7 - - - +
98A ILE* 1.3 65.6 + - - +
99A ILE* 4.6 4.9 - - + -
127A CYS* 4.1 1.1 - - - -
128A ASP* 3.2 21.5 - - + +
129A TYR* 3.7 26.7 - - - +
130A SER* 3.8 16.2 - - - +
388A LEU* 3.8 26.9 - - + -
392A LYS* 3.6 28.7 - - + -
402A ASP* 5.1 0.2 - - - +
463A ILE* 3.9 15.7 - - + -
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Residues in contact with ILE 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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65A ASP* 3.5 7.2 - - + -
68A THR* 3.8 33.2 - - + +
70A MET* 4.0 13.9 - - + -
83A PHE* 4.0 24.9 - - + -
87A THR* 3.8 23.6 - - + -
90A ALA* 4.3 14.6 - - + -
95A THR* 4.5 0.2 - - + -
97A MET* 1.3 79.1 - - - +
99A ILE* 1.3 64.1 + - - +
100A ASP* 4.8 1.6 - - + +
125A VAL* 5.1 0.2 - - + -
127A CYS* 4.5 4.0 - - - -
128A ASP 3.4 3.3 + - - +
129A TYR* 3.2 18.3 - - + +
130A SER 3.1 21.8 + - - +
352A VAL* 4.2 16.2 - - + -
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Residues in contact with ILE 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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64A ILE* 3.9 23.6 - - + -
65A ASP 2.9 14.3 + - - +
66A THR* 3.3 23.3 - - - +
68A THR* 3.5 13.8 + - - -
97A MET* 4.6 9.4 - - + -
98A ILE* 1.3 76.5 - - - +
100A ASP* 1.3 61.6 + - - +
101A PHE* 4.3 0.2 - - - -
130A SER* 3.3 22.0 - - - +
131A LEU 3.9 0.9 - - - +
132A HIS* 3.3 31.1 - - + +
386A PHE* 3.9 29.6 - - + -
388A LEU* 4.6 11.4 - - + -
465A ARG* 3.9 13.9 - - - +
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Residues in contact with ASP 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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68A THR* 2.9 28.6 + - - +
69A HIS* 3.7 7.8 - - - -
70A MET* 2.9 31.6 + - - +
83A PHE* 3.5 25.4 - - + -
98A ILE* 3.9 3.4 + - + -
99A ILE* 1.3 75.6 - - - +
101A PHE* 1.3 75.0 + - - +
117A TRP* 3.7 10.6 + - - -
129A TYR* 5.4 0.7 - - + -
130A SER 3.1 7.4 + - - +
131A LEU* 3.3 16.8 - - + -
132A HIS* 2.7 32.1 + - - -
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Residues in contact with PHE 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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66A THR 4.4 0.7 - - - -
67A HIS* 3.4 49.1 - + - -
68A THR 3.5 7.9 - - - -
69A HIS* 3.5 30.5 + + + +
99A ILE 4.3 0.2 - - - -
100A ASP* 1.3 84.4 + - - +
102A ALA* 1.3 59.4 + - - +
103A ILE* 3.6 15.3 + - + +
117A TRP* 3.0 27.5 + - - -
131A LEU* 4.6 0.7 - - - -
132A HIS* 3.4 42.6 - + + -
133A VAL 5.1 0.2 - - - -
134A ALA 5.5 0.9 - - - -
159A LYS* 3.5 33.0 - - + -
190A GLN* 3.7 17.5 - - - -
247A VAL* 4.6 1.6 - - + -
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Residues in contact with ALA 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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101A PHE* 1.3 68.4 - - - +
103A ILE* 1.3 59.9 + - - +
104A PRO* 3.3 6.3 - - - +
113A ALA* 4.0 8.7 - - + +
114A PHE* 4.0 29.4 - - - +
117A TRP* 3.7 15.9 - - + -
131A LEU* 4.6 5.8 - - + +
132A HIS 2.8 17.7 + - - +
133A VAL* 3.7 13.1 - - + +
134A ALA 3.1 22.5 + - - -
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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