Contacts of the strand formed by residues 3039 - 3045 (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 GLY3039 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30372 VAL* 6.0 0.2 - - - -
30382 GLY* 1.3 73.2 - - - -
30402 THR* 1.3 68.2 - - - +
30412 ILE* 3.6 8.3 + - - +
31022 SER 4.9 8.9 - - - +
31512 ILE* 5.5 6.5 - - - -
31522 CYS 2.5 16.0 + - - -
31532 VAL* 4.6 2.0 - - - +
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Residues in contact with THR3040 (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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30362 THR* 4.8 9.2 - - - +
30372 VAL* 3.5 19.1 + - + +
30382 GLY 2.9 24.2 + - - -
30392 GLY* 1.3 84.2 - - - +
30412 ILE* 1.4 68.2 - - - +
30422 LEU* 3.4 16.9 + - + +
31512 ILE* 3.3 5.7 - - - +
31522 CYS* 3.0 27.6 + - - -
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Residues in contact with ILE3041 (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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30392 GLY 4.4 7.4 - - - +
30402 THR* 1.4 75.4 - - - +
30422 LEU* 1.3 65.6 + - - +
30432 ARG* 3.3 3.4 - - - +
30442 SER* 3.6 33.0 - - - +
31022 SER* 3.3 34.1 - - - +
31492 ASP* 4.4 6.5 - - - +
31502 ILE 4.1 4.3 - - - +
31512 ILE* 4.7 7.4 - - + +
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Residues in contact with LEU3042 (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* 4.1 21.2 - - + +
30312 ALA 3.3 28.1 + - - +
30322 LEU* 3.6 31.6 - - + -
30332 PRO* 5.3 1.1 - - + -
30362 THR* 4.6 7.0 - - - +
30402 THR* 3.4 24.4 + - + +
30412 ILE* 1.3 74.3 - - - +
30432 ARG* 1.3 64.1 + - - +
30882 LEU* 4.1 13.5 - - + -
31502 ILE* 2.8 20.1 + - + +
31512 ILE 4.5 0.7 - - - -
31522 CYS* 3.9 24.5 - - + +
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Residues in contact with ARG3043 (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* 4.4 3.6 - - - -
30292 LYS 5.0 6.7 + - - -
30302 ILE* 4.5 13.0 - - + +
30412 ILE* 3.3 3.8 - - - -
30422 LEU* 1.3 84.5 - - - +
30442 SER* 1.3 65.6 + - - +
30452 ASP* 3.5 23.4 + - + +
30492 ASN* 3.4 24.7 + - - +
30502 PHE* 3.6 34.3 - - + -
30532 GLU* 2.9 37.2 + - - -
31482 CYS 3.7 1.7 - - - +
31502 ILE* 3.0 39.9 + - + +
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Residues in contact with SER3044 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30412 ILE* 3.6 21.4 - - - +
30432 ARG* 1.3 75.5 - - - +
30452 ASP* 1.3 63.1 + - - +
31022 SER* 4.9 0.9 + - - -
31472 HIS* 3.3 10.6 - - - -
31482 CYS 3.7 3.1 - - - -
31492 ASP* 2.5 36.8 + - - -
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Residues in contact with ASP3045 (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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30432 ARG* 3.5 22.1 + - + +
30442 SER* 1.3 75.3 - - - +
30462 LEU* 1.3 74.8 + - - +
30492 ASN* 3.1 33.5 - - - +
30502 PHE* 4.0 15.0 - - + -
31472 HIS* 2.7 39.5 + - - -
31482 CYS 3.4 12.3 + - - -
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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