Contacts of the strand formed by residues 159 - 167 (chain B) in PDB entry 3NMV
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 HIS 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B CYS 3.7 23.8 + - - -
110B VAL 4.2 1.6 - - - -
111B PRO* 3.6 35.8 - - + +
132B ILE 3.8 2.9 - - - -
133B PRO* 3.6 11.7 - - + -
134B ARG* 3.1 38.9 - - + +
135B PHE* 4.1 2.5 - - - -
157B SER* 3.5 16.1 + - - -
158B ALA* 1.3 76.3 - - - +
160B PHE* 1.3 60.1 + - - +
161B PHE* 3.5 25.0 - - + -
237B ALA 3.6 1.4 - - - +
238B VAL* 3.2 6.6 - - - -
239B VAL* 2.9 44.4 + - - +
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Residues in contact with PHE 160 (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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130B SER* 4.2 6.5 - - - -
131B THR 3.7 0.2 - - - -
132B ILE* 2.8 50.1 + - + +
135B PHE* 3.6 24.8 - + + -
159B HIS* 1.3 71.2 - - - +
161B PHE* 1.3 71.9 + - - +
162B GLY 4.0 11.0 - - - -
164B TYR* 3.4 26.9 - - - -
180B MET* 4.0 5.6 - - + -
181B HIS* 3.7 42.6 - + + -
184B LEU* 3.8 24.5 - - + -
236B VAL* 3.5 31.9 - - + -
237B ALA 3.6 2.0 - - - -
238B VAL* 4.4 3.8 - - + -
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Residues in contact with PHE 161 (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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111B PRO* 5.6 3.6 - - + -
113B TYR* 3.7 23.6 - + + -
130B SER 3.3 4.3 - - - +
131B THR* 3.6 29.4 - - + -
132B ILE 5.1 0.7 - - - -
133B PRO* 5.8 1.8 - - + -
159B HIS* 3.5 34.8 - + + -
160B PHE* 1.3 82.2 - - - +
162B GLY* 1.3 58.2 + - - +
236B VAL* 3.4 3.6 - - - +
237B ALA* 2.8 45.4 + - + +
239B VAL* 3.7 28.3 - - + -
332B LEU* 6.0 0.2 - - + -
334B LEU* 3.7 14.6 - - + +
407B VAL* 3.9 23.1 - - + -
409B VAL* 3.9 25.6 - - + -
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Residues in contact with GLY 162 (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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129B VAL* 3.3 4.9 - - - +
130B SER 2.7 37.3 + - - +
160B PHE* 4.0 3.2 - - - -
161B PHE* 1.3 75.4 - - - +
163B VAL* 1.3 67.5 - - - +
164B TYR* 3.8 23.1 - - - -
235B VAL 3.3 8.3 - - - -
236B VAL* 4.2 1.3 - - - -
334B LEU* 4.6 0.4 - - - -
407B VAL* 4.9 0.9 - - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B SER 3.6 6.5 - - - +
129B VAL* 4.3 6.5 - - + -
162B GLY* 1.3 78.8 - - - +
164B TYR* 1.3 70.0 + - - +
165B ASP 4.2 0.2 - - - -
233B THR* 4.3 2.1 + - - -
234B SER* 3.7 0.7 - - - -
235B VAL* 3.0 45.2 + - + +
252B SER* 4.6 2.2 - - - +
334B LEU* 4.0 23.8 - - + +
335B ALA* 4.1 2.0 - - - -
336B SER* 3.9 29.8 - - - +
405B SER* 4.2 15.0 - - - +
407B VAL* 3.9 24.0 - - + +
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Residues in contact with TYR 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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127B ASP* 3.4 2.9 - - - -
128B SER* 2.8 51.8 + - - +
130B SER* 3.8 21.1 - - - -
160B PHE* 3.4 30.0 - - - -
162B GLY* 3.8 10.3 - - - -
163B VAL* 1.3 83.8 - - - +
165B ASP* 1.3 58.7 + - - +
166B GLY 3.6 1.6 + - - -
173B ALA* 3.7 14.2 - - + +
176B CYS* 3.4 24.5 + - + -
177B ARG* 3.8 21.5 - - - -
180B MET* 3.4 15.9 - - + +
181B HIS* 5.6 0.2 - - - -
232B SER* 3.7 7.6 - - - +
233B THR 3.4 12.8 - - - +
234B SER* 3.4 25.6 - - - -
236B VAL* 3.7 9.6 - - + +
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Residues in contact with ASP 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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126B GLU 4.7 0.5 - - - +
127B ASP* 3.1 17.1 - - - +
163B VAL 4.2 0.4 - - - -
164B TYR* 1.3 71.1 - - - +
166B GLY* 1.3 70.8 + - - +
167B HIS* 4.0 3.5 + - - -
232B SER* 3.3 3.0 + - - -
233B THR* 2.9 46.7 + - + +
251B ASP* 4.4 0.9 - - - +
252B SER* 3.6 3.6 - - - +
336B SER* 4.0 4.5 - - - -
337B ASP* 2.9 7.3 - - - +
403B ASN* 5.6 0.5 - - - +
424B MG 2.3 28.9 - - - -
425B MG 2.7 23.8 - - - -
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Residues in contact with GLY 166 (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 GLU* 2.8 27.1 + - - +
164B TYR 3.6 1.2 + - - -
165B ASP* 1.3 82.7 + - - +
167B HIS* 1.3 61.1 + - - +
169B GLY 3.8 9.6 - - - -
173B ALA* 3.8 7.4 - - - -
231B GLY 3.3 11.9 - - - -
232B SER* 3.7 6.2 + - - -
426B MG 3.3 17.5 - - - -
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Residues in contact with HIS 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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89A SER* 3.5 8.7 - - - +
90A GLY* 4.3 17.0 - - - +
126B GLU* 4.0 0.7 - - - -
165B ASP* 4.0 4.8 + - - -
166B GLY* 1.3 76.4 - - - +
168B GLY* 1.3 61.9 + - - +
169B GLY 3.1 7.1 + - - -
229B THR 5.0 1.6 - - - -
230B VAL* 3.5 1.6 - - - +
231B GLY* 2.9 31.8 + - - +
232B SER* 3.6 20.9 - - - -
299B LEU* 3.8 17.6 - - + +
301B MET* 3.8 38.0 - - + +
304B SER* 4.1 0.4 - - - -
307B ASP* 2.6 40.3 + - - -
426B MG 4.5 0.4 - - - -
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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