Contacts of the helix formed by residues 580 - 587 (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 SER 580 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5442 GLU* 3.5 23.2 + - - -
5742 ALA 3.0 19.0 + - - -
5752 PHE* 3.0 34.7 - - - -
5772 SER* 2.8 35.5 + - - -
5792 LYS* 1.3 75.6 - - - +
5812 ARG* 1.3 64.1 + - - +
5822 GLN 3.0 1.6 - - - -
5832 GLU* 3.0 17.5 + - - +
5842 LEU 3.2 6.9 + - - -
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Residues in contact with ARG 581 (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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5752 PHE 4.7 7.1 + - - +
5772 SER 3.8 15.7 + - - +
5782 GLU* 5.2 2.5 - - - -
5792 LYS 4.9 1.8 - - - +
5802 SER* 1.3 80.8 + - - +
5822 GLN* 1.3 54.0 + - - +
5842 LEU* 2.9 12.4 + - - +
5852 ASN* 2.7 64.8 + - - +
5932 ARG* 4.8 15.8 - - - +
5962 VAL* 3.7 31.2 + - - +
5982 GLN* 4.3 23.4 - - - +
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Residues in contact with GLN 582 (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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5782 GLU 4.8 3.0 - - - +
5792 LYS* 3.1 42.7 + - - +
5812 ARG* 1.3 81.3 - - - +
5832 GLU* 1.3 54.5 + - - +
5852 ASN* 3.3 11.2 + - - +
5862 THR* 2.8 35.5 + - - +
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Residues in contact with GLU 583 (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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5112 THR* 4.7 1.2 + - - -
5432 GLY 4.2 3.5 - - - +
5442 GLU* 3.0 37.1 - - + +
5452 LYS* 3.1 19.0 + - - +
5522 TYR* 2.3 45.8 + - + +
5752 PHE* 5.0 3.7 - - + -
5792 LYS 3.6 4.5 + - - +
5802 SER* 3.0 11.9 + - - +
5822 GLN* 1.3 77.4 - - - +
5842 LEU* 1.3 65.2 + - + +
5862 THR* 3.3 14.4 + - - -
5872 ILE* 3.4 21.1 + - + +
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Residues in contact with LEU 584 (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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5412 THR* 3.7 20.2 - - + -
5682 VAL* 3.6 29.6 - - + +
5702 GLY* 3.5 23.1 - - - +
5752 PHE* 3.4 42.2 - - + -
5802 SER 3.2 4.5 + - - +
5812 ARG* 2.9 15.0 + - - +
5832 GLU* 1.3 80.4 - - + +
5852 ASN* 1.3 57.4 + - - +
5862 THR 2.9 9.3 + - - -
5872 ILE* 3.7 12.0 + - + +
5882 ALA 3.8 5.2 + - - -
5962 VAL* 3.4 32.6 - - + +
5982 GLN* 4.8 9.9 - - + -
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Residues in contact with ASN 585 (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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5812 ARG* 2.7 63.7 + - - +
5822 GLN* 3.3 9.2 + - - +
5842 LEU* 1.3 72.4 - - - +
5862 THR* 1.3 58.5 - - - +
5882 ALA* 4.3 5.1 - - - +
5902 LYS* 4.2 9.2 + - - -
5922 PRO* 3.9 34.7 - - + +
5962 VAL* 4.2 9.2 - - - +
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Residues in contact with THR 586 (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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5522 TYR* 4.0 36.1 - - + -
5562 ILE* 3.9 14.4 - - + +
5822 GLN* 2.8 25.4 + - - +
5832 GLU* 3.5 10.7 - - - -
5842 LEU 2.9 4.0 - - - -
5852 ASN* 1.3 77.9 - - - +
5872 ILE* 1.3 61.5 + - - +
5882 ALA 3.2 8.9 - - - +
5902 LYS* 4.3 9.1 + - - +
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Residues in contact with ILE 587 (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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5112 THR* 3.3 19.5 - - + -
5152 ILE* 3.4 20.9 - - + -
5392 VAL* 3.8 16.8 - - + -
5412 THR* 5.5 3.6 - - + -
5522 TYR* 3.2 42.0 - - + +
5562 ILE* 4.3 6.1 - - - -
5662 ARG* 2.6 41.8 + - - +
5682 VAL* 3.4 29.6 - - + -
5832 GLU* 3.4 19.6 + - + +
5842 LEU* 3.7 5.4 + - + +
5862 THR* 1.3 71.7 - - - +
5882 ALA* 1.3 58.8 + - - +
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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