Contacts of the helix formed by residues 603 - 618 (chain 2) in PDB entry 1BHQ
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 GLU 603 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4522 ARG* 3.1 48.2 + - - +
6012 ASN* 3.2 17.2 + - - +
6022 PHE* 1.3 75.1 - - - +
6042 ALA* 1.3 52.9 - - - +
6052 LEU 2.8 13.2 + - - -
6062 LYS* 3.3 26.5 - - - +
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Residues in contact with ALA 604 (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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5992 VAL* 2.8 24.0 - - + +
6002 ASN* 4.5 5.6 - - + +
6012 ASN* 2.9 23.9 + - - +
6032 GLU* 1.3 76.2 - - + +
6052 LEU* 1.3 56.2 + - - -
6062 LYS 3.2 1.1 - - - -
6072 THR* 2.5 41.4 + - + +
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Residues in contact with LEU 605 (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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4532 MET* 4.6 7.9 - - + -
4562 PHE* 3.0 54.1 - - + -
5402 ILE* 4.6 11.2 - - + -
5692 ILE* 3.4 30.1 - - + -
5712 VAL* 3.9 14.8 - - + -
5992 VAL* 3.6 24.2 - - + -
6012 ASN 4.4 3.4 - - - +
6022 PHE* 3.1 36.6 + - + +
6032 GLU 2.8 7.7 + - - -
6042 ALA* 1.3 71.2 - - - +
6062 LYS* 1.3 68.1 + - + +
6072 THR 3.0 3.5 + - - -
6082 ILE* 3.1 14.4 + - + +
6092 GLN 3.8 0.2 + - - -
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Residues in contact with LYS 606 (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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4522 ARG* 5.4 6.3 - - - -
4552 GLU* 3.9 32.0 + - - +
4562 PHE* 4.8 9.6 - - + +
4592 THR* 5.7 1.2 + - - -
6022 PHE 5.7 1.3 - - - -
6032 GLU* 3.3 18.4 - - - +
6052 LEU* 1.3 80.7 - - + +
6072 THR* 1.3 62.2 + - + +
6082 ILE 3.2 1.4 + - - -
6092 GLN* 2.9 50.5 + - - +
6102 ASN* 5.0 1.4 + - - -
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Residues in contact with THR 607 (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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5992 VAL* 4.4 2.3 - - - +
6042 ALA* 2.5 41.4 + - + +
6062 LYS* 1.3 78.8 - - + +
6082 ILE* 1.3 66.1 + - - +
6102 ASN* 5.4 0.8 - - - +
6112 GLN* 3.9 10.4 - - - +
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Residues in contact with ILE 608 (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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4562 PHE* 4.0 10.8 - - + -
5692 ILE* 3.5 48.7 - - + -
5972 PHE* 4.2 24.2 - - + -
5992 VAL* 4.0 20.4 - - + -
6052 LEU* 3.1 18.6 - - + +
6072 THR* 1.3 89.8 - - - +
6092 GLN* 1.3 58.1 + - - +
6102 ASN 3.1 3.4 - - - -
6112 GLN* 3.0 11.5 + - + +
6122 LEU* 2.8 32.9 + - + +
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Residues in contact with GLN 609 (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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4562 PHE* 3.6 27.1 - - + +
4592 THR* 3.2 32.1 - - - +
4602 VAL* 4.1 15.9 - - + +
4632 GLN* 3.4 15.7 + - - +
6062 LYS* 2.9 57.0 + - - +
6082 ILE* 1.3 78.3 - - - +
6102 ASN* 1.3 58.0 + - - +
6122 LEU* 3.9 1.1 - - - -
6132 ARG* 2.8 39.7 + - - +
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Residues in contact with ASN 610 (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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4632 GLN* 4.2 5.7 + - - +
6062 LYS 5.9 1.1 - - - -
6072 THR 5.4 1.0 + - - +
6082 ILE 3.1 0.6 - - - -
6092 GLN* 1.3 78.0 - - - +
6112 GLN* 1.3 79.7 - - - +
6132 ARG* 2.5 37.3 + - - +
6142 GLU* 2.9 25.3 + - - +
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Residues in contact with GLN 611 (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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5972 PHE* 3.8 22.0 - - + -
6072 THR 3.9 17.1 - - - +
6082 ILE* 3.0 10.2 + - + +
6102 ASN* 1.3 78.4 - - - +
6122 LEU* 1.3 55.7 + - - +
6132 ARG 2.5 16.6 + - - -
6142 GLU* 2.6 37.0 + - - +
6152 LYS* 3.0 19.9 + - - +
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Residues in contact with LEU 612 (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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4372 PHE* 5.2 0.2 - - + -
4562 PHE* 3.9 21.8 - - + -
4602 VAL* 4.7 12.1 - - + -
5382 VAL* 3.9 23.3 - - + -
5672 TYR* 4.2 11.9 - - + -
5692 ILE* 3.3 25.8 - - + -
5972 PHE* 3.9 28.8 - - + -
6082 ILE* 2.8 19.1 + - + +
6092 GLN* 4.3 3.4 - - - +
6112 GLN* 1.3 73.5 - - - +
6132 ARG* 1.3 57.4 + - - +
6152 LYS* 4.1 2.3 - - - +
6162 ILE* 3.0 56.1 + - + +
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Residues in contact with ARG 613 (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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4602 VAL* 5.2 3.1 - - + -
4632 GLN* 3.3 38.8 + - + +
4642 LEU* 3.3 34.7 - - + +
6092 GLN 2.8 18.5 + - - +
6102 ASN* 2.5 50.4 + - - +
6112 GLN 2.5 5.7 + - - -
6122 LEU* 1.3 73.3 - - - +
6142 GLU* 1.3 67.2 + - - +
6162 ILE 3.3 7.4 + - - -
6172 PHE* 3.4 24.9 + - + -
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Residues in contact with GLU 614 (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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6102 ASN* 2.9 16.4 + - - +
6112 GLN* 2.6 47.3 + - - +
6132 ARG* 1.3 77.0 - - - +
6152 LYS* 1.3 70.0 + - + +
6172 PHE* 3.3 8.2 + - - +
6182 ALA* 3.2 24.8 + - - +
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Residues in contact with LYS 615 (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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5672 TYR* 3.6 28.3 + - + +
5932 ARG 4.5 3.6 + - - -
5942 ASP* 3.0 49.6 + - + +
5962 VAL 5.7 0.6 + - - -
5972 PHE* 3.8 31.8 - - + -
6112 GLN* 3.0 19.7 + - - +
6122 LEU* 4.3 4.5 - - - +
6142 GLU* 1.3 85.9 - - + +
6162 ILE* 1.3 58.8 + - - +
6172 PHE 3.1 1.1 + - - -
6182 ALA* 3.7 15.8 + - - +
6192 ILE* 3.8 8.1 - - - +
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Residues in contact with ILE 616 (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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4332 SER* 5.4 1.9 + - - -
4352 ILE* 3.8 30.3 - - + +
4602 VAL* 5.4 0.2 - - + -
4642 LEU* 3.9 22.2 - - + -
4662 LYS* 4.9 1.9 + - - -
5362 ILE* 4.1 24.1 - - + +
5382 VAL* 3.8 19.7 - - + -
5672 TYR* 3.9 22.0 - - + -
6122 LEU* 3.0 38.6 - - + +
6132 ARG 3.3 6.5 + - - +
6152 LYS* 1.3 74.8 - - + +
6172 PHE* 1.3 64.4 + - + +
6192 ILE* 4.0 14.8 - - - +
6202 GLU* 5.0 2.4 - - - +
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Residues in contact with PHE 617 (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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4632 GLN 3.1 27.4 - - - -
4642 LEU* 3.3 38.6 - - + -
4652 LYS 5.7 0.4 - - - -
4662 LYS* 3.2 28.9 - - + +
6132 ARG* 3.4 26.8 + - + +
6142 GLU* 3.3 8.1 + - - +
6152 LYS 3.1 0.8 - - - -
6162 ILE* 1.3 81.8 - - - +
6182 ALA* 1.3 55.5 + - - +
6192 ILE 2.9 6.5 + - - -
6202 GLU* 2.9 3.5 + - - +
6212 GLY 2.5 47.7 + - - -
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Residues in contact with ALA 618 (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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6142 GLU 3.2 16.3 + - - +
6152 LYS* 3.7 9.6 - - - +
6172 PHE* 1.3 76.4 - - - +
6192 ILE* 1.3 61.2 + - + +
6202 GLU 3.2 3.5 + - - -
6212 GLY* 3.7 10.8 + - - -
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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