Contacts of the strand formed by residues 96 - 102 (chain D) in PDB entry 1OVM
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 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D SER 5.2 2.2 - - - +
59D ALA* 3.9 27.4 - - + +
60D ASP* 3.9 23.6 - - - +
63D ALA* 4.3 1.1 - - + -
69D ALA* 3.5 5.4 - - + +
71D LEU* 4.3 4.9 - - + -
86D ILE* 4.2 18.8 - - + +
89D SER* 3.6 25.8 - - - +
94D VAL* 2.9 15.8 + - + +
95D PRO* 1.3 76.6 - - - +
97D LEU* 1.3 72.9 + - - +
98D HIS 3.7 0.3 + - - -
156D MET* 4.3 2.0 - - - -
162D PRO* 3.1 9.7 - - + +
163D GLY 3.1 21.4 + - - +
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.4 1.1 - - + -
15D LEU* 3.5 32.3 - - + -
68D PHE* 4.1 5.8 - - + -
69D ALA 2.8 17.6 + - - +
70D ALA* 3.3 2.6 - - + -
71D LEU* 2.7 35.3 + - - +
95D PRO 4.1 0.2 + - - -
96D VAL* 1.3 72.9 - - - +
98D HIS* 1.3 61.4 + - - +
99D ILE* 3.9 18.8 - - + -
153D LEU* 3.9 14.1 - - + -
156D MET* 3.1 31.6 - - + -
163D GLY 3.7 10.3 - - - +
165D LEU* 4.1 27.8 - - + -
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Residues in contact with HIS 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LEU* 3.6 19.5 - - + +
73D THR* 2.7 34.7 + - - +
79D GLU* 3.8 32.0 - - + +
82D ALA* 4.2 11.9 - - + -
83D MET* 6.0 3.3 - - + +
86D ILE* 3.7 29.2 - - + +
96D VAL 3.7 0.4 + - - -
97D LEU* 1.3 74.0 - - - +
99D ILE* 1.3 69.9 + - - +
100D VAL* 4.0 1.9 + - + +
130D SER* 5.0 2.4 + - - -
134D THR* 6.0 0.2 - - + -
163D GLY 2.9 17.0 + - - +
164D TYR* 3.5 22.7 - + + -
165D LEU* 2.9 27.4 + - - +
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Residues in contact with ILE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.8 33.9 - - + -
15D LEU* 4.4 8.7 - - + -
23D LEU* 4.3 22.7 - - + -
34D PHE* 4.6 10.3 - - + -
70D ALA* 4.7 1.1 - - + -
71D LEU 2.7 12.4 + - - +
72D LEU* 3.1 21.7 - - + +
73D THR 2.9 25.1 + - - -
97D LEU* 3.9 27.4 - - + -
98D HIS* 1.3 76.6 - - - +
100D VAL* 1.3 62.8 + - - +
165D LEU* 3.5 12.6 - - + +
167D LEU* 4.3 18.6 - - + -
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D THR* 3.3 13.5 - - - +
74D THR 3.9 2.7 - - - +
75D PHE* 3.6 30.5 - - + +
79D GLU* 3.6 22.0 - - + +
98D HIS* 4.7 2.5 - - + +
99D ILE* 1.3 79.3 - - - +
101D GLY* 1.3 65.4 + - - +
102D ALA* 3.4 1.2 + - + -
164D TYR* 3.3 40.4 - - + +
165D LEU 3.0 12.8 + - - +
166D MET* 3.7 6.0 - - + +
167D LEU 2.9 25.9 + - - -
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Residues in contact with GLY 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D TYR* 3.5 23.1 - - - +
31D ASN* 4.1 11.7 - - - -
72D LEU* 4.4 4.7 - - - +
73D THR 3.0 13.0 + - - -
74D THR* 3.9 0.3 - - - -
75D PHE* 3.0 27.5 + - - +
99D ILE 4.1 1.0 - - - -
100D VAL* 1.3 70.4 - - - +
102D ALA* 1.3 58.8 + - - -
167D LEU* 3.5 10.3 - - - -
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D TYR* 3.9 7.4 + - - +
75D PHE* 3.9 11.2 - - + -
100D VAL 3.4 0.4 + - - +
101D GLY* 1.3 74.7 - - - +
103D PRO* 1.3 78.4 - - + +
108D GLN* 3.9 10.5 - - - +
166D MET* 3.7 30.3 - - + -
167D LEU 3.0 11.0 + - - +
168D PRO* 4.2 1.6 - - + -
169D ALA* 2.9 26.0 + - - +
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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