Contacts of the strand formed by residues 3072 - 3078 (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 ILE3072 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30252 ILE* 4.6 0.7 - - + -
30472 LEU* 4.1 5.4 - - + -
30512 LEU* 3.8 37.0 - - + -
30712 MET* 1.3 70.2 - - - +
30732 LYS* 1.3 59.7 + - - +
31262 SER* 3.3 2.5 - - - -
31272 PHE* 3.0 66.2 + - + -
31292 PRO* 4.2 10.3 - - + -
31362 TRP* 3.1 50.5 - - + +
31412 LEU* 4.0 7.6 - - + -
31702 TRP* 4.0 8.5 - - + -
31712 PHE 3.6 8.5 - - - +
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Residues in contact with LYS3073 (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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30202 MET* 2.6 41.4 - - + +
30712 MET 3.3 5.6 + - - +
30722 ILE* 1.3 72.2 - - - +
30742 MET* 1.3 61.6 + - - +
31242 THR* 4.1 19.9 - - + +
31252 MET 3.5 3.1 - - - -
31262 SER* 3.7 12.1 - - - +
31692 ASP 3.5 4.0 - - - +
31702 TRP* 3.5 4.4 - - - -
31712 PHE* 2.9 58.4 + - + +
31732 SER* 4.2 23.6 - - - +
4M C 3.8 19.1 + - - -
5M A 5.7 3.2 + - - -
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Residues in contact with MET3074 (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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30722 ILE 4.2 0.4 - - - -
30732 LYS* 1.3 74.6 - - - +
30752 VAL* 1.3 66.3 + - - +
30762 ALA* 4.5 2.0 - - + +
30902 CYS* 3.1 44.4 - - + -
31152 TRP* 5.0 0.7 - - + -
31232 MET* 2.8 47.1 - - + +
31242 THR* 3.1 31.9 - - - +
31252 MET* 2.8 28.0 + - + +
31272 PHE* 5.1 3.4 - - + -
31682 ILE* 3.8 23.8 - - + -
31692 ASP 3.4 4.3 - - - -
31702 TRP* 3.8 22.4 - - + -
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Residues in contact with VAL3075 (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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30202 MET* 4.9 6.5 - - + -
30732 LYS* 4.8 2.7 - - + -
30742 MET* 1.3 81.0 - - - +
30762 ALA* 1.3 65.7 + - - +
30772 THR* 5.1 4.4 - - - +
31222 ALA* 5.2 7.2 - - + -
31232 MET 3.3 9.6 - - - +
31242 THR* 3.9 17.9 - - + +
31672 THR 3.6 2.1 - - - +
31682 ILE* 3.3 2.0 - - - -
31692 ASP* 2.6 46.1 + - + +
31712 PHE* 3.1 34.5 - - + -
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Residues in contact with ALA3076 (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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30742 MET* 4.1 2.2 - - + -
30752 VAL* 1.3 74.6 - - - +
30772 THR* 1.3 75.1 + - - +
31152 TRP* 3.7 33.6 + - + -
31222 ALA* 3.2 23.2 - - - +
31232 MET* 2.9 22.2 + - + +
31662 VAL* 4.6 0.7 - - + -
31672 THR 3.6 4.0 - - - -
31682 ILE* 4.2 15.3 - - + +
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Residues in contact with THR3077 (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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30752 VAL* 5.1 5.2 - - - +
30762 ALA* 1.3 85.8 + - - +
30782 VAL* 1.3 66.8 + - - +
30792 GLY 5.5 0.4 - - - +
31152 TRP* 5.4 1.1 - - - +
31212 LYS 3.8 8.0 + - - +
31222 ALA* 3.8 14.1 - - - +
31652 GLN 4.0 2.6 - - - +
31662 VAL* 3.7 3.0 - - - +
31672 THR* 3.1 39.9 + - + +
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Residues in contact with VAL3078 (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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30322 LEU* 4.6 3.1 - - + -
30772 THR* 1.3 78.9 - - - +
30792 GLY* 1.3 69.3 + - - +
30802 ILE* 5.8 1.3 - - + -
30882 LEU* 5.3 0.7 - - + -
31152 TRP* 4.9 8.2 + - - +
31172 PRO* 3.2 39.6 - - + +
31202 THR 4.7 0.3 - - - +
31212 LYS* 4.0 13.4 + - - -
31562 TRP* 6.0 1.3 - - + -
31642 VAL* 3.1 35.9 - - + -
31652 GLN 3.7 7.6 - - - +
31662 VAL* 3.4 28.3 - - + -
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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