Contacts of the helix formed by residues 731 - 736 (chain B) in PDB entry 4HPF
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 LEU 731 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480B LEU* 4.2 3.6 - - + -
720B VAL* 4.3 7.0 - - + -
729B MET* 2.7 28.2 + - + +
730B GLY* 1.3 67.5 - - - -
732B ARG* 1.3 67.3 + - - +
733B ASN 3.1 1.3 - - - -
734B PHE* 2.9 20.1 + - + +
735B VAL* 3.1 11.1 + - - +
753B PHE* 3.8 27.1 - - + -
759B TYR* 5.3 0.4 - - + -
760B LEU* 3.7 30.7 - - + -
763B GLU* 3.3 24.8 + - + +
767B LEU* 3.6 24.4 - - + +
800B LEU* 4.1 22.7 - - + -
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Residues in contact with ARG 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B SER* 3.6 23.3 + - - +
453B HIS* 4.2 17.6 - - - +
689B PHE* 5.5 4.0 - - - -
730B GLY* 4.9 2.2 - - - -
731B LEU* 1.3 73.9 - - - +
733B ASN* 1.3 61.6 + - - +
734B PHE 2.8 7.8 + - - -
735B VAL 3.0 1.6 + - - -
736B MET* 2.9 56.5 + - + +
763B GLU* 4.9 1.0 + - - -
765B ARG* 5.6 3.0 - - - +
766B PHE* 3.9 55.1 + - + +
767B LEU* 3.4 16.5 - - + +
770B PHE* 4.3 9.4 - - + -
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Residues in contact with ASN 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B SER* 3.3 33.9 + - - +
476B ALA* 3.8 7.9 - - - +
477B GLU* 3.4 46.2 - - + +
480B LEU* 3.9 18.2 - - + +
481B GLY* 4.3 1.6 + - - -
730B GLY* 3.0 32.4 + - - +
731B LEU 3.1 0.4 - - - -
732B ARG* 1.3 77.6 - - - +
734B PHE* 1.3 56.3 + - - +
736B MET* 4.8 2.7 - - - -
737B PRO* 3.1 24.2 - - - +
928B THR* 6.0 0.5 - - - +
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Residues in contact with PHE 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B LEU* 3.8 41.0 - - + +
483B ILE* 3.9 23.8 - - + -
484B ALA* 3.8 9.4 - - - +
487B CYS* 4.3 4.3 - - - -
716B ILE* 4.3 12.8 - - + -
718B ALA* 3.9 28.7 - - + -
731B LEU* 2.9 14.1 + - + +
732B ARG 2.8 4.8 + - - -
733B ASN* 1.3 75.5 - - - +
735B VAL* 1.3 67.9 + - + +
737B PRO* 3.6 3.7 - - - +
738B LEU* 3.4 40.5 - - + +
751B ILE* 4.2 14.1 - - + -
753B PHE* 4.1 17.5 - + - -
798B ALA* 4.4 6.7 - - + -
800B LEU* 4.6 4.9 - - + -
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Residues in contact with VAL 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731B LEU 3.1 7.9 + - - +
732B ARG 3.0 5.4 + - - +
734B PHE* 1.3 77.0 - - + +
736B MET* 1.3 55.1 + - - +
738B LEU* 2.7 32.1 + - - +
739B ARG* 3.2 21.3 + - + -
751B ILE* 4.2 14.6 - - + -
753B PHE* 3.9 24.2 - - + -
767B LEU* 3.9 7.0 - - + -
770B PHE* 3.3 41.5 - - + -
773B ILE* 3.6 22.7 - - + -
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Residues in contact with MET 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688B MET* 5.9 1.6 - - - -
689B PHE* 3.5 44.1 - - + +
732B ARG* 2.9 42.7 + - + +
733B ASN* 4.8 2.5 - - - -
735B VAL* 1.3 75.7 - - - +
737B PRO* 1.3 63.3 - - + +
739B ARG* 2.9 26.6 + - - +
740B ALA* 3.5 3.1 + - - -
770B PHE* 3.7 27.1 - - + -
928B THR* 4.6 10.3 - - - +
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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