Contacts of the strand formed by residues 163 - 168 (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 GLY 163 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D VAL 3.1 6.7 + - - +
97D LEU* 3.9 6.3 - - - -
98D HIS* 2.9 27.9 + - - +
134D THR* 4.0 4.1 - - - +
136D ALA* 3.3 11.4 - - - -
152D VAL* 5.2 0.4 - - - -
156D MET* 3.5 26.1 - - - -
162D PRO* 1.3 74.8 - - - +
164D TYR* 1.3 61.8 + - - +
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Residues in contact with TYR 164 (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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75D PHE* 5.8 0.9 - - - -
79D GLU* 2.5 31.6 + - + -
83D MET* 5.8 0.7 - - + -
97D LEU* 4.4 0.6 - - - +
98D HIS* 3.5 25.4 - + + -
100D VAL* 3.3 26.4 - - + +
127D TYR* 3.5 45.1 + + - +
130D SER* 3.3 30.5 - - - -
134D THR* 3.8 11.7 - - + -
136D ALA 3.0 6.9 + - - -
137D GLN* 3.0 18.4 - - + +
138D ALA 3.0 24.9 + - - -
152D VAL* 4.4 2.3 - - - +
163D GLY* 1.3 75.6 - - - +
165D LEU* 1.3 70.8 + - - +
166D MET* 4.0 14.1 - - + +
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Residues in contact with LEU 165 (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* 3.9 30.5 - - + -
97D LEU* 4.1 15.7 - - + -
98D HIS 2.9 12.3 + - - +
99D ILE* 3.5 9.2 - - + +
100D VAL* 3.0 26.0 + - - +
138D ALA* 3.5 4.9 - - + -
140D LEU* 3.7 38.1 - - + -
149D ILE* 4.3 12.6 - - + -
152D VAL* 3.7 35.9 - - + -
153D LEU* 5.6 0.7 - - + -
164D TYR* 1.3 85.8 - - - +
166D MET* 1.3 61.9 + - - +
167D LEU 3.5 0.9 + - - -
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Residues in contact with MET 166 (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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75D PHE* 4.5 7.6 - - + -
100D VAL* 3.7 12.1 - - + +
102D ALA* 3.7 18.2 - - + -
108D GLN* 3.2 41.1 - - - +
123D PHE 4.4 15.0 - - - +
124D ARG* 4.8 3.4 - - - +
127D TYR* 5.3 6.1 - - - -
138D ALA 2.9 15.0 + - - +
139D VAL* 3.5 38.4 - - + -
140D LEU* 2.9 29.5 + - - +
164D TYR* 4.0 15.5 - - + +
165D LEU* 1.3 71.9 - - - +
167D LEU* 1.3 59.4 + - - +
168D PRO* 3.1 15.9 - - + +
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Residues in contact with LEU 167 (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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7D VAL* 4.4 7.2 - - + -
8D ALA* 5.1 2.9 - - - -
11D LEU* 4.2 13.7 - - + -
34D PHE* 3.9 36.8 - - + -
99D ILE* 4.3 14.4 - - + -
100D VAL 2.9 15.3 + - - +
101D GLY* 3.5 6.4 - - - -
102D ALA* 3.0 20.3 + - - -
140D LEU* 3.8 23.3 - - + -
165D LEU 3.5 1.0 + - - +
166D MET* 1.3 72.3 - - - +
168D PRO* 1.3 76.5 - - - +
169D ALA* 3.3 1.9 + - - -
171D VAL* 4.2 11.4 - - + -
172D ALA* 4.0 25.1 - - + +
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Residues in contact with PRO 168 (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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102D ALA 3.4 9.6 - - - +
103D PRO 3.5 13.9 - - - +
105D THR* 3.9 13.2 - - + +
108D GLN* 4.3 0.7 - - - +
139D VAL* 5.0 0.9 - - + -
140D LEU 3.2 24.9 - - - +
166D MET* 3.1 34.5 - - + +
167D LEU* 1.3 83.9 - - + +
169D ALA* 1.3 66.3 + - - +
170D ASP* 3.2 14.4 - - - +
171D VAL* 2.9 24.4 + - + +
172D ALA* 3.1 10.0 + - - +
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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