Contacts of the strand formed by residues 2111 - 2117 (chain 2) in PDB entry 1BMV
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 GLU2111 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20682 VAL 3.7 0.3 - - - +
20692 SER* 3.2 12.0 - - - -
20702 LYS* 3.0 40.2 + - + +
21062 PHE* 4.0 7.1 - - - -
21092 ILE 3.9 1.0 + - - +
21102 GLN* 1.3 76.8 - - - +
21122 LYS* 1.3 68.7 + - + +
31142 LEU* 3.4 8.6 - - - +
31152 TRP* 2.9 31.0 + - - -
31162 ASN* 2.9 12.2 + - + +
31192 CYS* 3.9 20.2 - - + +
31202 THR* 2.9 31.8 + - - -
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Residues in contact with LYS2112 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20672 GLU* 3.5 45.0 + - + +
20682 VAL 3.6 4.7 - - - +
20692 SER* 4.4 9.4 - - - +
21062 PHE* 4.1 0.8 - - - -
21102 GLN* 4.5 11.8 + - - +
21112 GLU* 1.3 89.2 - - + +
21132 VAL* 1.3 67.3 - - - +
21142 VAL* 4.1 8.1 + - + -
31132 GLU* 3.2 31.1 + - - +
31142 LEU 5.3 8.0 + - - +
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Residues in contact with VAL2113 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20672 GLU* 3.8 1.0 - - - -
20682 VAL* 2.8 37.6 + - + +
21042 VAL* 3.0 30.7 - - + -
21052 GLN 4.4 6.7 - - - +
21062 PHE* 2.7 42.2 - - + -
21102 GLN* 4.7 8.5 - - - +
21122 LYS* 1.3 76.6 - - - +
21142 VAL* 1.3 62.5 - - - +
21152 LEU* 3.7 21.8 - - + -
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Residues in contact with VAL2114 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20652 VAL* 4.8 13.7 - - + -
20662 PHE 3.7 6.5 - - - +
20672 GLU* 4.5 23.6 - - + +
21122 LYS* 4.1 8.6 + - + -
21132 VAL* 1.3 76.2 - - - +
21152 LEU* 1.3 76.0 + - - +
21162 LYS* 4.3 4.6 + - + +
21672 THR* 6.5 0.7 - - + -
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Residues in contact with LEU2115 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20642 LEU 4.2 0.5 - - - +
20652 VAL* 3.5 3.1 - - - +
20662 PHE* 2.7 48.9 + - + +
20682 VAL* 3.4 29.4 - - + -
20822 PHE* 3.9 29.2 - - + -
21022 LYS* 3.9 27.1 - - + -
21042 VAL* 4.0 11.2 - - + -
21132 VAL* 3.7 16.4 + - + -
21142 VAL* 1.3 86.7 - - - +
21162 LYS* 1.3 59.7 + - - +
21172 PHE* 4.1 15.4 - - + -
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Residues in contact with LYS2116 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20632 ASP* 4.2 18.6 + - + -
20642 LEU 4.0 2.2 - - - -
20652 VAL* 3.4 24.5 - - + +
21022 LYS* 2.9 24.9 + - - +
21142 VAL* 4.2 4.8 + - + -
21152 LEU* 1.3 73.4 - - - +
21172 PHE* 1.3 68.6 + - - +
21182 SER* 4.0 6.5 + - - +
21702 GLU* 3.1 28.2 + - - +
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Residues in contact with PHE2117 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20632 ASP* 3.5 5.4 - - - +
20642 LEU* 3.1 34.6 + - + +
20662 PHE* 3.9 27.1 - + + -
20822 PHE* 3.9 23.8 - + + -
20832 PHE* 4.2 12.6 - - - -
20842 ILE* 3.4 30.5 - - + -
21002 PRO 5.7 0.4 - - - -
21012 HIS* 6.1 0.2 - - - -
21022 LYS* 3.5 29.2 - - + +
21152 LEU* 4.1 17.3 - - + -
21162 LYS* 1.3 78.0 - - - +
21182 SER* 1.3 64.8 + - - +
21212 GLU* 3.0 27.6 - - - +
21222 PHE* 4.9 5.9 - - + -
21442 LEU* 4.0 14.8 - - + -
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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