Contacts of the helix formed by residues 4972 - 4977 (chain F) in PDB entry 6X34
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 ARG4972 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4965F TYR* 3.3 36.3 + - + +
4966F PHE 3.9 3.1 - - - -
4969F THR* 3.6 20.9 + - - +
4970F PRO 3.6 0.4 - - - -
4971F HIS* 1.3 76.6 - - - +
4973F PHE* 1.3 63.7 + - - +
4974F GLU 3.5 2.0 - - - -
4975F THR* 3.9 11.2 - - - -
4976F HIS* 3.3 23.6 + - - +
5026F PHE* 5.2 9.0 - - + -
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Residues in contact with PHE4973 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4223D SER* 5.1 16.4 - - - -
4964F ASP* 4.3 15.0 - - + +
4966F PHE* 3.7 22.6 - - + +
4970F PRO 3.8 22.9 - - - -
4971F HIS* 3.8 24.2 - + + -
4972F ARG* 1.3 80.2 - - - +
4974F GLU* 1.3 87.7 + - + +
4976F HIS* 3.9 9.0 + - - +
4977F THR* 4.3 6.8 + - - -
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Residues in contact with GLU4974 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4971F HIS 5.0 1.2 + - - +
4972F ARG 3.5 0.2 - - - -
4973F PHE* 1.3 97.3 - - + +
4975F THR* 1.3 65.8 + - - +
4976F HIS 3.2 2.8 + - - -
4977F THR* 3.5 9.4 + - - +
4978F LEU* 3.3 25.0 + - + +
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Residues in contact with THR4975 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4187F ARG* 5.7 0.3 + - - -
4971F HIS 4.0 18.0 + - - -
4972F ARG* 3.9 7.7 + - - -
4973F PHE 3.5 0.6 - - - -
4974F GLU* 1.3 75.2 - - - +
4976F HIS* 1.3 67.0 + - - +
4978F LEU* 3.6 11.8 + - - +
4979F GLU* 3.7 11.3 + - - +
4980F GLU* 4.3 4.3 + - - +
5026F PHE* 4.7 18.1 - - - -
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Residues in contact with HIS4976 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4959F CYS* 4.4 4.5 - - + -
4961F ILE* 3.4 14.3 - - + +
4962F GLY 4.4 3.5 + - - -
4963F SER 4.7 2.0 - - - -
4964F ASP* 4.4 13.4 - - + -
4965F TYR* 3.7 25.1 + - + +
4972F ARG 3.3 19.8 + - - +
4973F PHE 4.1 5.6 - - - +
4974F GLU 3.2 1.2 - - - -
4975F THR* 1.3 79.1 - - - +
4977F THR* 1.3 60.7 + - - +
4978F LEU 3.1 3.3 + - - -
4980F GLU 5.5 0.2 - - - +
4981F HIS* 2.6 69.8 + + + +
5025F CYS* 3.7 11.7 - - + +
5026F PHE* 4.8 9.7 - - - -
5101F ZN 2.3 29.3 - - - -
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Residues in contact with THR4977 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4973F PHE 4.3 6.0 + - - -
4974F GLU* 3.5 12.2 + - - +
4976F HIS* 1.3 79.1 - - - +
4978F LEU* 1.3 56.7 + - - +
4981F HIS 3.4 14.1 - - - -
4982F ASN* 3.4 20.9 - - - +
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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