Contacts of the strand formed by residues 101 - 112 (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 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B LYS* 3.8 22.8 - - + +
97B SER* 3.8 2.3 + - - -
98B ASP* 2.8 32.6 + - + +
99B THR 3.7 0.8 - - - -
100B SER* 1.3 81.1 - - - +
102B GLU* 1.3 63.2 + - - +
103B MET* 3.7 42.6 - - + -
181B PHE* 4.1 16.4 - - + -
182B LYS 3.5 15.5 - - - +
183B GLY* 4.2 5.4 - - - -
235B TYR* 5.2 2.7 - - + -
236B VAL* 3.4 23.8 - - + +
237B GLY* 3.8 16.8 - - - -
238B ASN* 4.6 4.3 - - - +
239B GLY 5.6 1.3 - - - +
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Residues in contact with GLU 102 (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 LYS 3.4 4.7 - - - +
97B SER* 4.1 15.4 - - - -
98B ASP 3.8 15.0 - - - +
99B THR 6.2 0.2 - - - -
101B LEU* 1.3 77.6 - - - +
103B MET* 1.3 66.2 + - - +
157B GLN* 4.7 10.0 + - - -
180B PHE* 3.8 16.9 - - + +
181B PHE* 3.7 1.4 - - - -
182B LYS* 2.8 71.8 + - + +
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Residues in contact with MET 103 (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 LEU 3.7 22.4 - - - +
94B PHE* 3.6 43.7 - - + -
95B ALA* 3.4 3.3 - - - -
96B LYS* 2.7 60.7 + - + +
101B LEU* 3.7 39.7 - - + -
102B GLU* 1.3 80.1 - - - +
104B THR* 1.3 62.6 + - - +
180B PHE* 3.5 4.0 - - - -
181B PHE* 4.2 7.0 - - + -
238B ASN* 5.9 5.6 - - + -
367B ASP* 5.4 3.8 - - - +
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Residues in contact with THR 104 (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 7.9 - - - -
95B ALA* 4.9 1.6 - - - +
103B MET* 1.3 75.5 - - - +
105B MET* 1.3 64.5 + - - +
155B LYS* 3.8 15.6 - - - +
157B GLN* 6.0 1.1 - - + -
178B TYR* 3.8 17.7 + - + -
179B ILE* 3.4 1.9 - - - -
180B PHE* 2.8 66.5 + - + +
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Residues in contact with MET 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 3.8 47.8 - - + +
47B SER* 4.2 8.3 - - - +
50B MET* 3.8 36.3 - - + -
90B LEU* 5.0 2.5 - - - +
91B HIS* 3.0 29.9 + - + +
94B PHE* 3.6 31.7 + - + +
95B ALA* 5.9 0.4 - - - +
104B THR* 1.3 78.5 + - - +
106B GLY* 1.3 58.4 + - - +
177B ASN* 4.3 4.0 - - - +
178B TYR* 3.4 22.4 + - - +
179B ILE* 4.2 15.3 - - + -
374B LEU* 6.3 0.7 - - - -
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Residues in contact with GLY 106 (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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91B HIS* 3.9 11.4 - - - -
105B MET* 1.3 77.7 - - - +
107B ASN* 1.3 64.1 + - - -
177B ASN* 3.4 7.4 + - - -
178B TYR* 3.0 56.9 + - - -
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Residues in contact with ASN 107 (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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50B MET* 3.6 26.3 - - - +
51B ALA* 4.7 1.4 + - - -
54B MET* 3.8 28.5 - - - +
91B HIS* 4.3 4.2 - - - -
106B GLY* 1.3 79.6 - - - -
108B ALA* 1.3 62.5 + - - +
129B TYR* 3.2 29.3 + - - +
130B GLU 4.3 3.1 + - - +
131B SER* 3.5 11.0 - - - +
132B GLU* 3.2 20.8 + - - +
151B TYR* 4.1 5.6 + - - -
175B LEU* 5.6 0.3 - - - +
176B VAL 3.3 7.1 - - - +
177B ASN* 2.7 28.3 + - - +
178B TYR* 4.2 1.0 - - - -
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Residues in contact with ALA 108 (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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54B MET* 5.3 1.3 - - - -
107B ASN* 1.3 76.2 - - - +
109B LEU* 1.3 61.2 + - - +
110B PHE* 3.9 15.0 - - + -
131B SER* 3.6 2.9 - - - -
132B GLU* 3.5 13.7 - - + +
134B LEU* 5.3 1.6 - - + -
151B TYR* 3.4 36.6 - - + +
174B VAL 3.8 0.5 - - - +
175B LEU* 3.6 3.3 - - - +
176B VAL* 2.7 44.1 + - + +
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Residues in contact with LEU 109 (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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54B MET* 4.4 5.4 - - + -
108B ALA* 1.3 72.7 - - - +
110B PHE* 1.3 66.2 + - - +
111B LEU* 3.7 34.6 + - + -
117B LEU* 4.5 12.8 - - + -
121B PHE* 5.1 8.1 - - + -
125B ILE* 4.6 15.9 - - + -
131B SER* 3.7 6.9 + - - +
132B GLU 2.6 14.7 + - - +
133B VAL* 3.5 7.1 - - + +
134B LEU* 2.9 27.6 + - - +
173B LEU* 3.9 33.9 - - + -
174B VAL 3.7 0.4 - - - +
175B LEU* 4.0 28.5 - - + -
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Residues in contact with PHE 110 (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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108B ALA* 3.9 14.1 - - + -
109B LEU* 1.3 74.4 - - - +
111B LEU* 1.3 60.6 + - - +
134B LEU* 3.5 32.1 - - + -
136B MET* 3.7 35.7 - - + -
138B PHE* 3.7 14.1 - - + -
147B GLN* 4.6 7.4 - - + -
148B ILE* 3.8 25.6 - - + -
151B TYR* 3.8 34.3 - + + -
173B LEU* 3.4 3.5 - - - -
174B VAL* 2.8 44.6 + - + +
176B VAL* 3.7 32.3 - - + -
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Residues in contact with LEU 111 (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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109B LEU* 3.7 13.2 + - + +
110B PHE* 1.3 74.3 - - - +
112B ASP* 1.3 64.5 + - - +
115B LEU* 3.4 49.1 - - + +
116B GLU* 4.2 0.4 - - - -
117B LEU* 3.8 31.0 - - + +
133B VAL* 4.7 9.9 - - + -
134B LEU 3.0 11.7 + - - +
135B ALA* 3.4 4.6 - - - -
136B MET* 2.6 32.4 + - - +
138B PHE* 3.7 4.4 - - - -
172B ILE 3.8 0.7 - - - +
173B LEU* 3.8 28.9 - - + -
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Residues in contact with ASP 112 (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 LEU* 1.3 77.2 - - - +
113B GLY* 1.3 66.5 + - - +
114B SER* 2.5 28.6 + - - +
115B LEU* 2.9 31.1 + - + +
135B ALA* 5.8 0.2 - - - +
136B MET 3.3 10.2 - - - +
137B ASN* 4.1 4.9 - - - +
138B PHE* 3.4 27.4 + - + -
139B GLN* 4.8 3.4 + - - +
172B ILE* 2.9 41.8 + - + +
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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