Contacts of the strand formed by residues 3023 - 3032 (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 LEU3023 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30162 PRO* 3.1 26.9 - - + +
30172 LYS* 3.0 4.7 - - - +
30182 GLY* 2.5 59.0 - - - +
30192 SER 2.9 9.3 + - - +
30202 MET* 4.0 7.9 - - - +
30222 ASP* 1.3 78.0 - - - +
30242 LYS* 1.3 56.0 + - - +
30252 ILE 3.7 0.2 + - - -
30582 ALA* 3.8 7.9 - - + -
31712 PHE* 3.4 2.6 - - - +
31722 ILE* 2.7 82.0 + - + +
31732 SER 4.4 5.4 - - - +
31742 SER* 5.4 3.4 - - - +
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Residues in contact with LYS3024 (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 3.9 0.6 + - - +
30212 LEU* 3.2 22.9 + - + +
30222 ASP 3.3 3.2 + - - -
30232 LEU* 1.3 74.3 - - - +
30252 ILE* 1.3 56.6 + - - +
30262 SER 4.1 8.4 + - - +
30272 GLN* 3.9 11.7 - - - +
30562 PHE* 2.2 74.9 - - + +
30572 ARG* 5.5 0.2 - - + -
30582 ALA* 3.2 5.2 + - - -
31692 ASP* 3.0 34.1 + - - -
31702 TRP 3.6 16.2 - - - +
31712 PHE* 3.7 26.8 - - + -
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Residues in contact with ILE3025 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30232 LEU 3.7 0.6 + - - +
30242 LYS* 1.3 77.1 - - - +
30262 SER* 1.4 68.4 + - - +
30512 LEU* 3.0 42.0 - - + +
30542 GLY 3.8 2.9 - - - +
30562 PHE* 4.5 0.9 - - - -
30582 ALA 4.6 1.8 - - - +
30592 SER* 2.9 28.0 + - - +
30622 LEU* 3.6 36.4 - - + +
30722 ILE* 4.5 6.1 - - + -
31362 TRP* 4.4 7.9 - - + -
31702 TRP* 3.1 18.2 + - + +
31712 PHE 4.1 2.9 - - - +
31722 ILE* 2.9 47.3 - - + +
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Residues in contact with SER3026 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30242 LYS* 3.8 9.3 - - - +
30252 ILE* 1.4 72.6 - - - +
30272 GLN* 1.4 61.8 + - - +
30502 PHE 3.6 3.8 - - - -
30512 LEU* 2.8 37.3 - - - -
30532 GLU 3.9 8.5 - - - -
30562 PHE* 4.1 12.3 - - - -
31692 ASP* 4.0 2.3 - - - +
31702 TRP* 2.5 65.6 + - - +
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Residues in contact with GLN3027 (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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30242 LYS* 3.9 9.5 - - - +
30262 SER* 1.4 76.2 - - - +
30282 SER* 1.3 63.6 + - - +
30292 LYS* 4.0 17.9 + - + +
30532 GLU* 3.1 25.6 + - - +
30562 PHE* 3.6 29.2 - - + -
31672 THR* 4.1 21.1 - - + +
31682 ILE 3.6 4.5 - - - +
31692 ASP* 3.4 23.9 + - - +
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Residues in contact with SER3028 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30272 GLN* 1.3 75.2 - - - +
30292 LYS* 1.3 61.0 - - - +
30302 ILE* 4.0 3.4 - - - -
30432 ARG* 4.4 3.4 - - - -
30502 PHE* 3.3 22.5 + - - -
30532 GLU* 3.2 17.4 + - - -
31672 THR* 3.4 2.9 - - - +
31682 ILE* 2.5 46.7 + - - +
31702 TRP* 2.5 36.6 + - - -
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Residues in contact with LYS3029 (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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30272 GLN* 4.0 18.5 + - + +
30282 SER* 1.3 76.7 - - - +
30302 ILE* 1.3 63.5 + - - +
30312 ALA 4.3 0.2 + - - -
30432 ARG* 5.0 6.9 + - - -
30532 GLU* 4.7 1.9 + - - +
31652 GLN* 2.8 38.5 - - - +
31662 VAL 3.7 2.7 - - - -
31672 THR* 3.2 20.4 - - + +
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Residues in contact with ILE3030 (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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30282 SER* 4.7 8.5 - - - -
30292 LYS* 1.3 80.5 - - - +
30312 ALA* 1.4 59.9 + - - +
30422 LEU* 4.1 33.2 - - + +
30432 ARG* 4.5 8.7 - - + +
30502 PHE* 4.2 6.7 - - + -
30882 LEU* 5.9 0.2 - - + -
31502 ILE* 2.9 54.7 - - + -
31652 GLN* 3.2 8.9 - - - +
31662 VAL* 2.7 54.1 + - + +
31682 ILE* 4.1 19.1 - - + -
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Residues in contact with ALA3031 (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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30292 LYS 4.3 0.2 + - - -
30302 ILE* 1.4 74.2 - - - +
30322 LEU* 1.3 59.0 + - - +
30332 PRO* 2.9 20.5 - - + +
30422 LEU* 3.3 24.0 + - - +
31642 VAL 3.8 4.9 - - - +
31652 GLN* 4.5 6.1 - - + +
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Residues in contact with LEU3032 (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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30302 ILE 4.0 0.8 + - - -
30312 ALA* 1.3 70.4 - - - +
30332 PRO* 1.3 67.9 - - - +
30342 LYS* 3.2 4.7 + - - -
30362 THR* 4.2 14.6 - - + +
30422 LEU* 3.6 25.6 - - + -
30782 VAL* 4.6 2.9 - - + -
30862 ILE* 4.3 27.8 - - + -
30882 LEU* 3.5 26.0 - - + -
31522 CYS* 5.4 0.2 - - + -
31562 TRP* 4.2 13.5 - - + +
31642 VAL* 2.6 46.9 + - + +
31652 GLN 4.5 0.2 - - - +
31662 VAL* 3.4 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