Contacts of the strand formed by residues 3111 - 3115 (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 ASP3111 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30922 MET* 3.2 26.8 + - + +
30932 ASN* 5.5 0.4 - - - +
31082 CYS 4.9 0.6 + - - -
31092 SER 4.0 0.2 - - - -
31102 GLN* 1.3 106.4 + - - +
31122 CYS* 1.3 59.6 + - - +
31252 MET* 3.4 20.4 - - + +
31262 SER 4.6 3.9 - - - +
31272 PHE* 4.0 32.3 - - + +
31282 ASN 5.0 6.2 + - - +
31462 PHE* 6.0 0.3 - - - -
31802 ARG* 2.9 24.9 + - - +
2M G 5.2 12.3 + - - +
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Residues in contact with CYS3112 (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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21652 LYS* 3.5 20.9 + - - +
30892 ALA* 4.8 7.4 - - - -
30902 CYS 2.9 18.2 - - - +
30912 ALA* 3.6 13.9 - - - -
31042 ILE* 4.6 12.3 - - - -
31072 ILE* 3.8 10.8 - - - +
31082 CYS* 3.7 32.1 + - - -
31102 GLN 4.4 0.2 - - - -
31112 ASP* 1.3 73.2 - - - +
31132 GLU* 1.4 77.9 + - - +
31142 LEU* 4.8 2.0 - - - -
31252 MET* 4.1 3.6 - - - -
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Residues in contact with GLU3113 (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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20672 GLU* 4.6 5.7 - - - +
21122 LYS* 3.2 27.1 + - - +
21652 LYS* 5.9 1.2 + - - -
30892 ALA* 3.3 21.3 - - - -
30902 CYS 3.4 8.8 + - - -
31122 CYS* 1.4 85.1 - - - +
31142 LEU* 1.3 69.1 + - - +
31152 TRP* 3.6 9.9 - - + -
31232 MET* 3.3 30.7 - - + +
31252 MET* 4.3 10.3 - - - +
2M G 3.6 25.2 + - - -
3M U 4.3 14.1 + - - +
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Residues in contact with LEU3114 (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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20142 TRP* 4.2 10.8 - - + -
20692 SER* 4.3 20.8 + - - +
20702 LYS 5.3 1.3 - - - +
20712 MET* 2.9 42.8 - - + -
21112 GLU* 3.4 9.9 - - - +
21122 LYS* 5.3 7.8 + - - +
30872 ALA* 4.2 8.5 - - + -
30882 LEU 3.3 10.5 - - - +
30892 ALA* 4.0 9.2 - - + -
31042 ILE* 4.0 16.4 - - + -
31122 CYS* 4.8 2.5 - - - -
31132 GLU* 1.3 79.3 - - - +
31152 TRP* 1.3 65.0 + - - +
31532 VAL* 3.3 29.4 - - + -
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Residues in contact with TRP3115 (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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21112 GLU* 2.9 9.2 - - - +
30742 MET* 5.3 0.2 - - + -
30762 ALA* 3.7 31.9 + - + +
30772 THR* 6.0 0.4 - - - +
30782 VAL* 4.9 6.3 + - - +
30862 ILE 4.3 0.2 - - - -
30872 ALA* 4.6 2.7 - - - -
30882 LEU* 2.9 60.0 + - + -
30892 ALA* 4.0 15.7 - - - -
30902 CYS* 4.1 12.1 - - + -
31132 GLU* 3.6 19.3 - - + -
31142 LEU* 1.3 78.8 - - - +
31162 ASN* 1.3 58.3 + - - +
31172 PRO* 3.3 21.1 - - - +
31202 THR* 3.4 41.3 + - + -
31212 LYS 5.9 0.8 - - - -
31222 ALA 5.8 0.4 - - - +
31232 MET* 4.2 29.7 - - + +
31502 ILE* 5.5 4.7 - - + -
31662 VAL* 4.2 19.1 - - + -
31682 ILE* 5.3 6.7 - - + -
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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