Contacts of the strand formed by residues 128 - 133 (chain B) in PDB entry 2VL3
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 PHE 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B LEU* 3.9 20.2 - - + -
37B PHE* 3.2 8.4 - - - +
38B GLY* 2.8 51.4 + - - +
51B HIS* 4.3 0.5 - - - -
73B LEU* 5.1 2.2 - - + -
104B PHE* 3.6 24.7 - + - -
110B LEU* 4.0 22.0 - - + -
125B LEU* 4.3 14.6 - - + -
126B LYS 3.3 21.8 - - - -
127B ARG* 1.3 75.9 - - - +
129B SER* 1.3 66.0 + - - +
130B MET* 3.5 34.1 - - + -
140B LEU* 4.8 0.2 - - + -
141B ASN 3.1 14.6 - - - +
142B VAL* 4.1 15.3 - - + -
152B SER* 3.8 8.6 - - - -
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Residues in contact with SER 129 (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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36B LEU 3.4 5.8 - - - -
37B PHE* 3.8 10.5 - - - -
55B PHE* 4.3 2.9 - - - -
128B PHE* 1.3 75.7 - - - +
130B MET* 1.3 64.9 + - - +
140B LEU* 3.8 1.6 - - - +
141B ASN* 2.8 54.6 + - - +
151B CYS 3.8 0.3 + - - -
152B SER* 3.2 33.7 + - - -
157B ILE* 3.7 15.7 - - - +
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Residues in contact with MET 130 (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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3B ILE* 4.7 4.7 - - + -
9B ILE* 3.4 31.4 - - + -
35B VAL* 3.3 5.5 - - - -
36B LEU* 2.9 57.6 + - + +
104B PHE* 4.7 2.2 - - + -
110B LEU* 4.4 11.7 - - + -
128B PHE* 3.5 21.8 - - + -
129B SER* 1.3 75.9 - - - +
131B VAL* 1.3 60.0 + - - +
132B VAL* 3.8 7.0 - - + -
137B VAL* 4.0 14.1 - - + -
139B ALA 3.1 16.2 - - - +
140B LEU* 3.4 25.6 - - + -
141B ASN* 4.9 0.4 - - - +
157B ILE* 3.7 8.7 - - - +
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Residues in contact with VAL 131 (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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33B LYS* 5.0 8.5 - - + -
34B GLY 3.5 7.4 - - - +
35B VAL* 4.8 0.7 - - + -
130B MET* 1.3 72.2 - - - +
132B VAL* 1.3 64.3 + - - +
133B GLN* 6.0 0.2 - - + -
137B VAL* 3.7 2.3 - - - -
138B LYS* 2.8 45.1 + - + -
139B ALA* 3.1 27.2 + - + +
157B ILE* 3.5 28.5 - - + -
160B GLN* 4.4 11.4 - - + +
161B LEU* 3.8 31.9 - - + -
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Residues in contact with VAL 132 (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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9B ILE* 4.3 12.6 - - + -
29B PHE* 3.8 35.9 - - + +
32B LYS 4.3 0.4 - - - +
33B LYS* 3.5 6.8 - - - +
34B GLY 2.8 31.1 + - - +
36B LEU* 4.7 1.3 - - + -
130B MET* 3.8 31.2 - - + +
131B VAL* 1.3 80.4 - - - +
133B GLN* 1.3 64.1 + - - +
134B ASP 4.8 0.2 - - - +
135B GLY* 3.5 36.6 - - - +
136B ILE 3.3 6.5 - - - +
137B VAL* 4.7 2.0 - - - -
138B LYS* 4.4 2.2 - - - -
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Residues in contact with GLN 133 (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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31B GLY 4.8 3.8 + - - -
32B LYS* 3.2 25.4 + - - +
33B LYS* 3.4 29.2 - - + +
68B GLN* 5.3 0.6 + - - -
131B VAL* 6.0 0.4 - - + -
132B VAL* 1.3 73.6 - - - +
134B ASP* 1.3 72.8 + - + +
135B GLY 2.8 5.0 + - - -
136B ILE* 2.9 29.1 + - - +
138B LYS* 3.5 28.0 + - + +
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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