Contacts of the strand formed by residues 173 - 184 (chain B) in PDB entry 2VDY
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 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 5.6 2.0 - - + -
109B LEU* 3.9 33.2 - - + -
110B PHE 3.4 3.8 - - - -
111B LEU* 3.8 19.3 - - + -
115B LEU* 5.3 0.7 - - + -
117B LEU* 4.5 0.4 - - + -
121B PHE* 5.8 0.4 - - + -
171B ALA* 4.3 0.7 - - - +
172B ILE* 1.3 88.0 - - + +
174B VAL* 1.3 65.3 + - - +
175B LEU* 4.1 14.1 - - + +
312B ILE* 3.7 37.0 - - + -
318B LEU* 3.9 8.7 - - + -
344B LEU* 4.6 4.9 - - + +
345B GLU* 3.5 3.1 - - - -
346B ALA* 2.8 51.3 + - + -
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 3.8 0.9 - - - +
109B LEU* 3.7 1.0 - - - -
110B PHE* 2.8 50.0 + - + +
138B PHE* 3.8 23.1 - - + -
148B ILE* 4.2 6.1 - - + -
164B PHE* 3.8 37.2 - - + -
171B ALA* 4.0 11.2 - - + -
173B LEU* 1.3 81.3 - - - +
175B LEU* 1.3 63.8 + - - +
176B VAL* 4.0 19.3 - - + -
343B PHE* 4.2 7.4 - - + -
344B LEU 3.4 7.0 - - - +
345B GLU* 4.3 2.7 - - + -
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ALA* 3.7 34.8 - - + +
54B MET* 3.8 32.5 - - + -
55B LEU* 3.9 41.1 - - + -
107B ASN* 5.6 0.4 - - - +
108B ALA 3.7 2.7 - - - -
109B LEU* 4.0 13.2 - - + -
121B PHE* 5.9 2.7 - - + -
173B LEU* 4.1 5.6 - - + +
174B VAL* 1.3 71.8 - - - +
176B VAL* 1.3 69.9 + - - +
177B ASN* 5.4 0.2 - - + -
342B MET* 3.8 0.8 - - + +
343B PHE* 3.1 8.8 - - - +
344B LEU* 2.8 47.2 + - + +
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASN* 3.3 5.5 - - - +
108B ALA* 2.7 41.5 + - + +
110B PHE* 3.7 30.7 - - + -
148B ILE* 4.2 9.6 - - + -
151B TYR* 4.2 15.5 - - + -
152B VAL* 4.0 24.0 - - + -
163B LEU* 4.9 1.3 - - + -
174B VAL* 4.0 12.8 - - + -
175B LEU* 1.3 86.2 - - - +
177B ASN* 1.3 71.2 + - - +
178B TYR* 4.9 2.7 - - + +
342B MET 3.4 7.2 - - - +
343B PHE* 4.3 7.0 - - + -
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Residues in contact with ASN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 2.9 36.9 + - - +
50B MET* 3.4 28.5 - - - +
51B ALA* 3.8 21.5 - - + +
105B MET* 4.3 3.6 - - - +
106B GLY 3.4 7.9 + - - -
107B ASN* 2.7 24.5 + - - +
175B LEU* 4.8 0.4 - - - +
176B VAL* 1.3 80.0 - - - +
178B TYR* 1.3 79.2 + - - +
341B ALA* 3.2 4.9 - - - +
342B MET* 2.9 33.1 + - + +
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Residues in contact with TYR 178 (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 THR* 3.8 24.8 + - + -
105B MET* 3.4 11.6 + - - +
106B GLY* 3.0 65.7 + - - -
107B ASN* 5.2 0.4 - - - -
132B GLU* 5.5 0.3 + - - -
151B TYR* 3.5 32.0 + + - -
152B VAL* 5.4 4.5 - - + -
155B LYS* 3.4 57.5 + - + +
156B THR* 4.0 13.5 - - + -
176B VAL* 5.2 3.1 - - + -
177B ASN* 1.3 80.7 + - - +
179B ILE* 1.3 65.7 + - - +
340B GLY 3.4 8.7 - - - +
341B ALA* 4.7 3.4 - - + -
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER* 3.4 22.2 - - - +
46B VAL* 3.8 26.9 - - + -
47B SER* 3.9 9.6 - - - -
94B PHE* 3.7 33.0 - - + -
104B THR 3.4 4.9 - - - +
105B MET* 4.2 15.0 - - + +
156B THR* 4.3 2.4 - - - +
178B TYR* 1.3 78.2 - - - +
180B PHE* 1.3 63.7 + - - +
339B ALA* 3.3 4.8 - - - +
340B GLY* 2.8 50.9 + - - +
374B LEU* 4.6 4.9 - - + -
375B PHE* 4.1 18.2 - - + -
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Residues in contact with PHE 180 (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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94B PHE* 3.6 4.6 - - - -
102B GLU* 4.1 20.6 - - + -
103B MET* 3.5 5.2 - - - -
104B THR* 2.8 58.3 + - + +
155B LYS 4.2 7.0 - - - +
156B THR* 3.3 29.8 - - - -
157B GLN* 3.8 27.4 - - + -
159B LYS* 3.9 15.5 - - + -
179B ILE* 1.3 74.3 - - - +
181B PHE* 1.3 66.3 + - - +
182B LYS* 4.0 29.2 - - + -
337B GLU* 4.4 16.4 - - + -
338B ALA 3.7 2.7 - - - -
339B ALA* 3.9 11.0 - - + -
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Residues in contact with PHE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PHE* 3.9 23.3 - + + -
101B LEU* 4.1 20.0 - - + -
102B GLU 3.7 0.9 - - - -
103B MET* 4.2 9.6 - - + -
180B PHE* 1.3 80.4 - - - +
182B LYS* 1.3 63.5 + - - +
183B GLY* 3.9 19.7 - - - -
235B TYR* 3.7 44.6 - + - -
239B GLY* 4.9 7.2 - - - -
336B THR* 4.4 14.8 - - + -
337B GLU* 3.5 2.9 - - - +
338B ALA* 2.7 41.3 + - + +
365B ILE* 4.4 9.0 - - + -
374B LEU* 4.9 9.2 - - + -
375B PHE* 3.7 27.8 - + + -
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Residues in contact with LYS 182 (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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100B SER 4.1 1.0 - - - +
101B LEU* 3.5 9.5 - - - +
102B GLU* 2.8 71.0 + - + +
157B GLN* 6.1 1.0 - - - +
180B PHE* 4.0 11.6 - - + -
181B PHE* 1.3 74.9 - - - +
183B GLY* 1.3 58.8 + - - +
336B THR 3.4 3.8 - - - +
337B GLU* 3.7 40.5 + - + +
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Residues in contact with GLY 183 (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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101B LEU* 4.2 9.4 - - - -
181B PHE* 3.9 13.3 - - - -
182B LYS* 1.3 77.2 - - - +
184B THR* 1.3 62.6 + - - -
235B TYR* 3.6 18.4 - - - -
335B GLY* 3.2 2.4 - - - -
336B THR 2.8 37.2 + - - +
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Residues in contact with THR 184 (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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99B THR 4.8 1.0 + - - -
100B SER* 2.7 36.6 + - - +
183B GLY* 1.3 73.4 - - - -
185B TRP* 1.3 69.6 + - - +
188B PRO* 6.0 2.0 - - + -
235B TYR* 3.3 4.9 - - - -
236B VAL* 2.9 38.6 + - + +
334B GLU* 3.4 21.5 - - + +
335B GLY* 4.2 0.2 - - - -
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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