Contacts of the strand formed by residues 163 - 171 (chain B) in PDB entry 3OYP
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 163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B PRO* 3.9 27.4 - - + -
130B ARG 3.4 11.2 - - - +
131B PRO* 4.3 2.5 - - + -
159B CYS* 3.3 4.9 - - - +
160B THR 3.0 36.3 + - - +
161B ARG* 4.1 6.5 - - + +
162B GLY* 1.3 80.1 - - - +
164B ALA* 1.3 62.7 + - - +
165B LYS* 3.9 15.9 + - - +
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU* 3.9 6.2 - - + +
129B PRO* 3.4 5.5 - - - +
130B ARG 2.6 38.5 + - - +
132B VAL* 4.2 6.2 - - - +
135B LEU* 4.0 26.7 - - + -
157B ALA* 4.4 7.4 - - + -
158B VAL 3.4 11.7 - - - +
159B CYS* 3.9 13.9 - - - -
163B VAL* 1.3 72.3 - - - +
165B LYS* 1.3 60.8 + - - +
166B ALA 4.7 1.8 - - - +
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B SER* 3.7 4.0 - - - -
126B LEU* 2.9 33.7 + - - +
129B PRO* 4.7 13.7 - - + -
158B VAL* 3.1 10.9 + - + +
159B CYS 5.6 0.7 - - - -
160B THR* 3.5 39.3 + - - +
163B VAL* 4.4 20.2 - - + +
164B ALA* 1.3 76.4 - - - +
166B ALA* 1.3 62.8 + - + +
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ARG* 6.2 0.2 - - + -
123B ARG* 4.7 13.0 - - + +
124B GLY 3.3 14.4 - - - +
125B SER* 3.9 10.5 - - - +
126B LEU* 4.0 3.1 - - - +
157B ALA* 3.6 5.4 - - - +
158B VAL* 3.0 44.4 + - + +
164B ALA* 3.8 2.0 - - - +
165B LYS* 1.3 81.3 + - + +
167B VAL* 1.3 66.1 + - - +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.1 11.7 - - + -
116B VAL* 3.8 24.7 - - + -
123B ARG* 3.5 9.7 - - - +
124B GLY* 2.7 48.3 + - - +
126B LEU* 3.5 20.6 - - + -
135B LEU* 4.2 6.7 - - + -
143B LEU* 4.3 16.6 - - + -
154B PHE* 3.5 33.7 - - + -
156B ALA 3.7 2.2 - - - -
157B ALA* 5.0 0.7 - - + -
158B VAL* 5.5 1.3 - - - -
166B ALA* 1.3 76.8 - - - +
168B ASP* 1.3 59.8 + - - +
169B PHE* 4.2 1.0 + - + -
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Residues in contact with ASP 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B SER* 3.4 16.7 + - - +
123B ARG* 4.7 13.3 + - + +
154B PHE* 3.5 5.4 - - - -
155B ARG* 2.7 57.6 + - - +
156B ALA* 2.5 33.5 + - + +
157B ALA* 4.5 2.1 - - - +
167B VAL* 1.3 73.6 - - - +
169B PHE* 1.3 77.0 + - - +
3F 0Y8 4.3 7.9 - - - +
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Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 4.2 9.4 - - + -
118B ARG* 3.5 28.0 - - - -
121B ASP 3.4 20.9 - - - -
122B SER* 3.1 29.9 + - - -
123B ARG* 3.4 37.2 - - - -
124B GLY* 4.0 0.9 - - - -
143B LEU* 3.3 39.7 - - + -
151B VAL* 4.4 9.2 - - + -
152B GLY* 4.0 7.0 - - - -
153B ILE 3.1 14.6 - - - +
154B PHE* 5.3 0.2 - - + -
155B ARG* 4.0 3.8 + - - +
167B VAL* 4.4 3.8 - - + -
168B ASP* 1.3 84.0 + - - +
170B ILE* 1.3 74.8 + - - +
171B PRO* 4.3 7.2 - - + -
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B VAL* 4.5 6.3 - - + -
80B GLN* 3.5 16.2 - - + +
81B ASP 3.6 24.7 - - - +
82B LEU* 4.0 38.6 - - + -
152B GLY* 2.9 3.3 - - - -
153B ILE* 2.7 48.7 + - + +
155B ARG* 3.4 38.1 - - + +
169B PHE* 1.3 71.5 - - - +
171B PRO* 1.3 77.9 - - + +
174B SER* 4.3 8.3 - - - +
175B MET* 4.6 2.2 - - - +
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Residues in contact with PRO 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 5.0 2.5 - - - +
121B ASP* 3.7 25.4 - - + +
122B SER* 4.2 11.0 - - - -
151B VAL 3.6 7.9 - - - +
152B GLY* 4.1 1.1 - - - -
155B ARG* 5.0 3.4 - - - +
169B PHE* 3.6 11.9 - - + +
170B ILE* 1.3 92.7 - - + +
172B VAL* 1.3 63.3 + - - +
173B GLU* 3.1 26.9 + - + +
174B SER* 3.3 26.5 + - - +
175B MET* 4.2 2.4 - - - +
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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