Contacts of the helix formed by residues 790 - 794 (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 ASN 790 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710B TYR* 3.2 19.5 - - - +
711B LYS* 4.2 8.5 - - - +
712B PHE* 3.2 37.0 + - + +
715B HIS* 3.3 15.1 - - + -
787B HIS 3.0 13.8 + - - -
788B ALA 3.8 8.4 + - - +
789B ALA* 1.3 76.7 - - - +
791B ILE* 1.3 62.7 + - - +
792B GLU* 3.0 16.2 + - - -
793B GLN* 3.1 34.7 + - - +
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Residues in contact with ILE 791 (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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717B VAL* 4.6 10.1 - - + -
786B LEU* 3.2 56.1 - - + +
787B HIS* 4.1 4.0 - - + +
789B ALA* 3.1 4.8 + - + +
790B ASN* 1.3 76.1 - - - +
792B GLU* 1.3 67.4 + - - +
793B GLN 3.4 0.2 - - - -
794B CYS* 3.4 27.9 - - - -
797B CYS* 3.9 23.8 - - + -
824B ILE* 4.2 17.7 - - + -
827B LEU* 3.9 19.1 - - + -
859B VAL* 3.8 19.8 - - + +
860B PRO* 5.4 0.2 - - - +
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Residues in contact with GLU 792 (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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787B HIS* 2.9 47.6 + - + +
790B ASN* 3.2 11.5 + - - -
791B ILE* 1.3 91.6 + - + +
793B GLN* 1.3 73.6 + - + +
794B CYS 3.3 4.6 + - - +
827B LEU* 5.5 0.9 - - + -
828B GLN 5.1 0.2 - - - +
829B ILE* 4.1 25.8 - - + -
859B VAL* 4.9 9.2 - - - +
860B PRO* 5.8 3.5 - - - +
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Residues in contact with GLN 793 (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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711B LYS* 3.7 29.2 - - - +
712B PHE 3.7 9.0 - - - +
713B ARG* 3.6 24.6 + - - +
714B ASN* 3.0 22.9 + - - -
715B HIS* 3.7 1.2 + - - -
790B ASN* 3.1 36.5 + - - +
792B GLU* 1.3 103.2 + - + +
794B CYS* 1.3 60.5 + - - +
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Residues in contact with CYS 794 (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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714B ASN* 4.3 3.8 - - - +
715B HIS* 3.3 35.0 - - + +
717B VAL* 4.1 8.3 - - + -
790B ASN 3.5 0.8 + - - +
791B ILE* 3.4 24.2 - - - +
792B GLU 3.3 6.0 - - - +
793B GLN* 1.3 81.6 - - - +
795B SER* 1.3 63.0 + - - +
796B MET* 3.5 25.1 - - - -
797B CYS* 4.1 4.0 - - - -
859B VAL* 4.3 6.7 - - - -
860B PRO* 4.1 17.2 - - - +
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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