Contacts of the strand formed by residues 120 - 127 (chain B) in PDB entry 3VAS
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 THR 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B PRO 4.2 6.3 - - - +
17B LEU 4.6 0.9 - - - +
89B ILE* 4.5 5.4 - - + +
90B GLY* 2.7 25.9 + - - +
92B ASP* 2.6 35.6 + - - +
94B GLN* 3.9 18.1 - - + +
95B GLY* 3.2 9.2 + - - +
98B ILE* 3.9 26.0 - - + -
119B MET* 1.3 74.9 - - - +
121B GLY* 1.3 76.9 + - - +
122B LYS* 3.8 9.7 + - - +
137B TYR* 5.4 1.7 - - - -
140B ALA* 4.0 2.0 - - - -
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Residues in contact with GLY 121 (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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15B PRO 4.5 3.2 + - - -
16B LEU* 3.6 13.8 - - - -
17B LEU* 3.0 19.6 + - - +
88B CYS 5.6 0.4 + - - -
119B MET 3.3 4.3 + - - -
120B THR* 1.3 85.2 - - - +
122B LYS* 1.3 60.0 + - - +
137B TYR* 3.2 15.7 - - - -
138B LEU 3.2 19.9 + - - -
139B GLY* 4.2 1.3 - - - -
140B ALA* 4.0 3.2 - - - +
141B ALA 4.8 0.6 - - - +
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Residues in contact with LYS 122 (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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16B LEU* 4.0 1.0 - - - +
17B LEU* 3.2 17.0 - - + +
19B ILE* 4.0 20.4 - - + +
49B TYR* 3.6 47.5 + - + +
50B ASP* 5.8 0.8 + - - -
53B GLN* 5.9 4.4 - - - +
94B GLN* 6.3 2.0 - - + -
120B THR 4.4 7.4 - - - +
121B GLY* 1.3 76.6 - - - +
123B VAL* 1.3 67.3 + - - +
124B ALA 4.2 0.2 - - - -
136B THR* 4.1 0.5 - - - +
137B TYR* 2.8 52.1 + - + +
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Residues in contact with VAL 123 (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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16B LEU* 3.7 19.1 - - + -
17B LEU 2.9 9.1 + - - -
18B ASP* 3.4 21.5 - - - +
19B ILE* 2.8 31.9 + - - +
49B TYR* 4.5 1.1 - - - -
122B LYS* 1.3 79.4 - - - +
124B ALA* 1.3 64.2 - - - +
125B VAL* 3.3 10.5 + - + +
134B MET* 3.7 33.0 - - + -
135B VAL 3.4 5.2 - - - +
136B THR* 3.6 24.9 - - - +
401B ADN 3.7 12.8 - - + +
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Residues in contact with ALA 124 (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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19B ILE* 4.0 4.5 - - - -
48B ILE* 4.1 25.6 - - + -
49B TYR* 3.8 18.4 - - + -
52B ILE* 3.9 21.8 - - + -
123B VAL* 1.3 68.7 - - - +
125B VAL* 1.3 59.0 + - - +
126B LEU* 3.8 3.9 - - + +
133B SER 3.4 2.6 - - - +
134B MET* 3.3 5.4 - - - -
135B VAL* 2.8 36.8 + - + +
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Residues in contact with VAL 125 (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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18B ASP* 3.9 14.6 - - + -
19B ILE 3.0 9.5 + - - +
20B ILE* 3.7 32.2 - - + -
21B VAL* 3.1 26.2 + - - +
52B ILE* 5.2 0.2 - - - +
123B VAL* 3.6 24.0 - - + +
124B ALA* 1.3 71.9 - - - +
126B LEU* 1.3 62.2 + - - +
127B VAL* 3.6 4.1 + - + +
132B ARG* 3.7 36.6 - - + +
133B SER 3.7 2.0 - - - +
134B MET* 4.1 17.5 - - + -
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Residues in contact with LEU 126 (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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21B VAL* 3.8 13.0 - - + -
23B ALA* 3.6 13.2 - - + -
27B MET* 3.7 38.1 - - + -
28B TYR* 3.4 23.7 + - + +
33B LEU* 3.8 24.5 - - + -
48B ILE* 3.7 25.1 - - + -
52B ILE* 4.7 1.1 - - + -
124B ALA* 4.1 14.6 - - + +
125B VAL* 1.3 73.5 - - - +
127B VAL* 1.3 62.2 + - - +
132B ARG* 3.2 6.4 - - - -
133B SER* 2.8 40.3 + - - +
135B VAL* 5.4 0.2 - - + -
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Residues in contact with VAL 127 (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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20B ILE* 3.8 20.6 - - + -
21B VAL 2.9 16.1 + - - +
22B ASP* 3.5 19.2 - - - +
23B ALA 3.1 21.2 + - - +
28B TYR* 3.7 1.1 + - - -
125B VAL* 3.9 3.4 - - + +
126B LEU* 1.3 76.0 - - - +
128B SER* 1.3 65.9 + - - +
131B LEU 3.6 15.3 - - - +
132B ARG* 3.5 38.6 - - + +
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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