Contacts of the strand formed by residues 163 - 172 (chain B) in PDB entry 1DVM
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 LEU 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 5.3 3.8 - - + -
49B THR* 5.8 0.2 - - + -
97B ILE* 3.7 24.5 - - + -
98B PHE 3.3 14.4 - - - +
99B VAL* 4.1 13.0 - - + -
161B THR* 4.0 1.3 - - - +
162B ARG* 1.3 82.4 - - - +
164B VAL* 1.3 62.2 + - - +
165B LEU* 6.5 0.2 - - + -
306B PHE* 3.8 39.9 - - + -
309B LEU* 4.2 7.9 - - + -
315B LEU* 3.8 23.6 - - + -
316B HIS 3.6 17.6 + - - +
317B VAL* 3.9 8.1 - - + +
318B ALA* 2.8 36.0 + - - +
319B LEU 3.3 1.2 + - - -
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Residues in contact with VAL 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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96B ALA 4.0 0.3 - - - +
97B ILE* 3.4 6.5 - - - +
98B PHE* 2.7 65.2 + - + +
126B PHE* 3.6 20.2 - - + -
136B ILE* 3.8 19.5 - - + -
157B VAL* 5.3 1.1 - - + -
161B THR* 4.6 5.2 - - + -
163B LEU* 1.3 76.2 - - - +
165B LEU* 1.3 62.0 + - - +
166B VAL* 4.0 22.0 - - + -
317B VAL* 5.7 0.2 - - - -
319B LEU* 3.3 30.1 - - + +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.8 38.8 - - + +
43B LEU* 4.5 8.3 - - + -
46B LEU* 3.5 42.8 - - + -
96B ALA 3.5 6.3 - - - +
97B ILE* 4.5 10.3 - - + +
163B LEU* 6.5 0.2 - - + -
164B VAL* 1.3 73.6 - - - +
166B VAL* 1.3 72.4 + - - +
167B ASN* 4.9 0.2 - - + -
286B LEU* 4.9 5.6 - - + -
317B VAL* 4.8 6.7 - - + +
319B LEU 2.6 15.5 + - - +
320B ALA* 4.2 17.5 - - + -
321B LEU* 2.9 32.6 + - - +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.9 2.6 - - - +
94B THR* 5.3 2.2 - - + -
95B ASP* 3.4 3.1 - - - -
96B ALA* 2.7 52.3 + - + +
98B PHE* 4.8 1.6 - - + -
136B ILE* 3.9 22.0 - - + -
140B VAL* 3.5 29.8 - - + -
151B LEU* 3.8 26.9 - - + -
164B VAL* 4.0 13.2 - - + -
165B LEU* 1.3 81.5 - - - +
167B ASN* 1.3 69.0 + - - +
168B ALA* 4.7 1.8 - - + +
321B LEU* 3.6 7.4 - - + -
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Residues in contact with ASN 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY* 3.1 22.7 + - - -
42B VAL* 3.8 17.5 - - + -
93B THR* 5.6 1.4 - - - -
94B THR 3.2 9.3 + - - +
95B ASP* 2.9 25.9 + - - -
151B LEU* 5.6 0.3 - - - +
165B LEU* 4.9 0.9 - - + -
166B VAL* 1.3 76.7 - - - +
168B ALA* 1.3 61.8 + - - +
169B LEU* 3.5 13.5 - - - +
286B LEU* 5.6 0.9 - - + -
321B LEU 3.0 12.2 + - - +
322B GLN* 2.7 41.5 + - + +
323B LYS 2.8 24.6 + - - -
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Residues in contact with ALA 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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93B THR* 3.3 0.7 - - - -
94B THR* 2.7 48.6 + - + +
140B VAL* 3.4 35.2 - - + -
144B THR* 4.0 8.5 - - + +
148B ILE* 4.5 5.2 - - + -
151B LEU* 5.2 0.7 - - + -
166B VAL* 4.9 1.3 - - + -
167B ASN* 1.3 75.2 - - - +
169B LEU* 1.3 64.2 + - - +
323B LYS* 3.2 13.7 - - + +
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Residues in contact with LEU 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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35B SER* 2.9 37.9 - - - +
37B TYR* 5.0 6.5 - - + -
38B GLY* 4.2 3.8 - - - +
91B ILE* 4.6 0.7 - - + -
92B SER 2.8 14.8 - - - +
93B THR* 3.7 20.4 - - + -
144B THR* 4.4 1.6 - - - -
148B ILE* 3.6 5.7 - - - +
167B ASN* 3.5 31.2 - - - +
168B ALA* 1.3 81.8 - - - +
170B TYR* 1.3 59.5 + - - +
323B LYS 3.1 6.5 + - - -
324B VAL* 3.3 19.0 - - + +
325B LYS 3.2 21.1 + - - -
371B LEU* 4.8 1.8 - - + +
372B PHE* 3.5 23.8 - - + -
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Residues in contact with TYR 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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89B ASP 4.8 7.0 - - - -
90B GLU 4.0 6.3 - - - -
91B ILE* 3.1 10.0 - - - +
92B SER* 2.6 46.8 + - - -
144B THR* 4.8 2.2 - - - +
147B MET* 3.5 52.1 - - + +
148B ILE* 4.5 6.1 - - + -
169B LEU* 1.3 73.7 - - - +
171B PHE* 1.3 62.5 + - - +
172B ASN* 3.2 34.9 + - + +
325B LYS* 3.4 32.8 - - + +
327B GLU* 2.5 42.4 + - - -
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Residues in contact with PHE 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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90B GLU* 3.0 32.8 - - + -
91B ILE* 4.2 7.6 - - + -
170B TYR* 1.3 78.8 - - - +
172B ASN* 1.3 64.3 + - - +
173B GLY 4.2 4.5 - - - -
228B TYR* 3.4 44.4 - + - -
233B LEU* 3.7 30.7 - - + -
325B LYS 2.8 10.3 + - - +
326B ILE* 3.2 32.9 - - + +
327B GLU* 3.0 24.4 + - - +
362B VAL* 3.9 13.0 - - + -
371B LEU* 6.2 0.4 - - + -
372B PHE* 3.3 35.2 - + + -
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Residues in contact with ASN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLU* 2.7 17.8 + - - +
170B TYR* 3.2 32.4 + - + +
171B PHE* 1.3 77.7 - - - +
173B GLY* 1.3 77.9 + - - +
327B GLU* 3.3 17.7 + - - +
329B ASN* 3.0 21.8 + - - +
332B GLY 4.2 3.6 + - - -
333B THR* 2.9 47.9 - - + +
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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