Contacts of the helix formed by residues 754 - 759 (chain A) in PDB entry 1N54
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 HIS 754 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A HIS* 3.8 21.3 + + + -
645A ILE* 3.4 33.3 - - + +
646A ARG* 4.6 15.7 - - + -
649A ASN* 3.1 25.5 + - - +
710A PHE* 3.7 26.9 - + + -
750A ILE* 3.2 17.3 + - + +
753A GLN* 1.3 95.9 + - + +
755A HIS* 1.3 66.3 + - - +
756A GLN* 3.3 3.4 - - - -
757A ILE* 3.2 15.3 + - + +
758A ILE* 3.2 16.6 + - + +
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Residues in contact with HIS 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A MET* 3.7 36.3 - - + +
363A PRO* 4.2 11.1 - - + +
364A ALA* 6.3 0.4 - - - +
751A PHE 3.1 21.2 + - - +
752A LEU* 2.9 25.6 - - - -
753A GLN 3.4 4.7 + - - -
754A HIS* 1.3 74.8 - - - +
756A GLN* 1.3 96.5 + - + +
757A ILE 3.0 1.0 + - - -
758A ILE* 3.1 13.5 + - - +
759A GLN* 3.2 27.1 + - - +
785A PHE* 3.8 18.2 - - + -
788A LEU* 4.6 8.5 - - + -
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Residues in contact with GLN 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753A GLN 5.2 0.9 + - - +
754A HIS 3.3 1.5 + - - -
755A HIS* 1.3 100.0 + - + +
757A ILE* 1.3 70.1 + - + +
759A GLN* 3.9 26.6 + - - +
760A GLN* 4.5 5.4 - - - +
789A GLN* 5.9 1.0 + - - -
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Residues in contact with ILE 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A ASN* 4.1 27.6 - - + +
652A VAL* 6.1 2.0 - - + -
653A LEU* 6.2 5.2 - - + -
706A GLN* 3.7 25.8 - - - +
710A PHE* 4.4 10.5 - - + -
754A HIS* 3.2 11.3 + - + +
755A HIS 3.2 0.6 - - - -
756A GLN* 1.3 81.3 - - + +
758A ILE* 1.3 60.2 + - - +
760A GLN* 2.8 51.7 + - - +
761A TYR* 3.3 23.7 - - + +
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Residues in contact with ILE 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A PHE* 3.9 32.5 - - + -
714A PHE* 4.1 8.5 - - + -
750A ILE 3.6 21.3 - - - +
751A PHE* 4.0 23.8 - - + -
754A HIS 3.4 16.6 - - - +
755A HIS* 3.1 7.5 + - - +
757A ILE* 1.3 70.4 - - - +
759A GLN* 1.3 51.5 + - - +
760A GLN 2.6 17.4 + - - -
761A TYR* 2.7 29.4 + - + +
765A LEU* 3.4 27.0 - - + +
785A PHE* 3.5 21.3 - - + -
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Residues in contact with GLN 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A MET* 6.1 0.3 - - - +
755A HIS* 3.3 31.2 + - - +
756A GLN* 3.9 24.2 + - - +
757A ILE 3.1 0.4 + - - -
758A ILE* 1.3 75.6 - - - +
760A GLN* 1.3 61.0 + - + +
761A TYR 3.2 0.4 - - - -
762A MET* 3.3 28.8 + - + +
785A PHE* 4.0 16.9 - - + -
789A GLN* 3.3 41.2 + - + +
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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