Contacts of the strand formed by residues 102 - 112 (chain A) 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 GLU 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A LYS 3.5 9.4 - - - +
97A SER* 4.1 17.9 - - - -
98A ASP 5.0 4.7 - - - +
101A LEU* 1.3 77.3 - - - +
103A MET* 1.3 66.4 + - - +
104A THR* 6.0 1.3 - - + -
157A GLN* 4.1 20.7 + - - +
180A PHE* 3.8 23.7 - - + +
181A PHE* 3.7 1.2 - - - -
182A LYS* 2.8 64.5 + - + +
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Residues in contact with MET 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU 4.1 5.6 - - - +
94A PHE* 3.0 52.4 - - + +
95A ALA* 3.5 1.0 - - - -
96A LYS* 2.7 56.5 + - + +
101A LEU* 5.0 8.5 - - + -
102A GLU* 1.3 77.8 - - - +
104A THR* 1.3 67.9 - - - +
179A ILE* 5.3 7.6 - - + -
180A PHE* 3.4 13.9 - - - +
181A PHE* 4.3 23.3 - - + -
367A ASP* 6.2 1.8 - - - -
374A LEU* 4.6 16.4 - - + -
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Residues in contact with THR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PHE 3.3 5.6 - - - -
95A ALA* 4.8 4.2 - - - +
102A GLU* 6.0 1.3 - - + -
103A MET* 1.3 78.0 - - - +
105A MET* 1.3 68.4 + - - +
155A LYS 3.9 16.4 - - - +
157A GLN* 6.0 1.3 - - + -
178A TYR* 4.1 12.8 + - + -
179A ILE* 3.5 5.2 - - - +
180A PHE* 2.9 58.4 + - + +
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Residues in contact with MET 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 3.8 20.4 - - + +
47A SER* 3.8 35.4 - - - +
50A MET* 3.9 30.7 - - + -
91A HIS* 3.0 27.5 + - + +
94A PHE* 3.6 42.2 + - + -
95A ALA* 5.5 1.5 - - - +
104A THR* 1.3 80.4 + - - +
106A GLY* 1.3 61.1 + - - +
177A ASN* 4.3 4.5 - - - +
178A TYR* 3.4 18.8 + - - +
179A ILE* 4.1 16.4 - - + -
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Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A HIS* 3.7 11.2 - - - -
105A MET* 1.3 77.1 - - - +
107A ASN* 1.3 69.2 + - - +
177A ASN* 3.4 2.6 + - - -
178A TYR* 3.0 56.9 + - - -
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Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A MET* 3.6 25.8 - - - +
51A ALA* 4.9 0.9 - - - -
54A MET* 3.7 28.1 - - - +
91A HIS* 3.9 4.9 - - - -
106A GLY* 1.3 74.5 - - - -
108A ALA* 1.3 63.2 + - - +
129A TYR* 2.9 38.4 + - - +
130A GLU 4.0 4.0 + - - +
131A SER* 3.4 6.8 - - - -
132A GLU* 3.3 17.2 + - - +
151A TYR* 4.2 5.7 + - - -
175A LEU* 5.9 0.3 - - - +
176A VAL 3.4 6.0 - - - +
177A ASN* 2.8 30.9 + - - +
178A TYR* 4.1 3.6 - - - -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A MET* 4.5 4.0 - - - +
107A ASN* 1.3 76.2 - - - +
109A LEU* 1.3 61.3 + - - +
110A PHE* 4.1 15.0 - - + -
131A SER* 3.5 4.0 - - - -
132A GLU* 3.4 13.2 - - + +
134A LEU* 4.7 2.0 - - + -
151A TYR* 3.5 35.2 - - + +
174A VAL 4.0 0.2 - - - +
175A LEU* 3.7 2.3 - - - -
176A VAL* 2.8 38.5 + - + +
178A TYR* 5.7 0.2 - - + -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A MET* 4.7 5.2 - - + -
108A ALA* 1.3 73.6 - - - +
110A PHE* 1.3 75.8 + - - +
111A LEU* 3.8 19.5 + - + -
117A LEU* 4.3 14.6 - - + -
121A PHE* 4.9 8.7 - - + -
125A ILE* 4.4 12.3 - - + -
131A SER* 4.2 6.1 - - - +
132A GLU 2.8 13.4 + - - +
133A VAL* 3.5 10.9 - - + +
134A LEU* 2.9 28.6 + - - +
173A LEU* 3.9 38.4 - - + -
174A VAL 3.6 5.6 - - - +
175A LEU* 4.1 22.2 - - + -
312A ILE* 6.4 0.2 - - + -
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Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA* 4.1 13.0 - - + -
109A LEU* 1.3 75.0 - - - +
111A LEU* 1.3 59.8 + - - +
134A LEU* 3.5 34.3 - - + +
136A MET* 4.0 19.1 - - + +
147A GLN* 4.1 27.6 - - + -
148A ILE* 3.8 36.6 - - + -
151A TYR* 3.7 34.3 - + + -
172A ILE 4.1 0.2 - - - +
173A LEU* 3.4 5.2 - - - -
174A VAL* 2.8 46.2 + - + +
176A VAL* 3.8 24.2 - - + -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 3.8 7.9 - - + -
110A PHE* 1.3 74.8 - - - +
112A ASP* 1.3 69.9 + - - +
113A GLY* 3.6 0.3 + - - -
115A LEU* 3.5 46.0 - - + +
116A GLU* 4.4 0.9 - - - +
117A LEU* 3.8 35.9 - - + +
133A VAL* 4.6 11.2 - - + -
134A LEU 3.0 11.0 + - - +
135A ALA* 3.5 5.9 - - - -
136A MET* 2.9 29.0 + - - +
172A ILE 3.9 1.8 - - - +
173A LEU* 3.9 26.9 - - + -
312A ILE* 5.8 0.2 - - + -
313A THR* 6.1 0.7 - - + -
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 1.3 78.0 - - - +
113A GLY* 1.3 61.4 + - - +
114A SER* 2.6 32.3 + - - +
115A LEU* 3.0 27.4 + - + +
136A MET* 3.1 12.8 - - - +
137A ASN* 3.7 6.1 - - - +
138A PHE* 3.0 49.1 + - + -
139A GLN* 5.1 0.7 - - - +
172A ILE* 2.9 34.7 + - + +
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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