Contacts of the helix formed by residues 4972 - 4977 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4965B TYR* 3.3 37.0 + - + +
4966B PHE 3.9 3.1 - - - -
4968B THR* 5.2 0.2 - - - +
4969B THR* 3.6 20.9 + - - +
4970B PRO 3.6 0.4 - - - -
4971B HIS* 1.3 77.3 - - - +
4973B PHE* 1.3 63.8 + - - +
4974B GLU 3.5 1.3 - - - -
4975B THR* 3.9 11.0 - - - -
4976B HIS* 3.3 23.7 + - - +
5026B PHE* 5.2 9.2 - - + -
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Residues in contact with PHE4973 (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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4964B ASP* 4.3 15.2 - - + +
4966B PHE* 3.7 22.4 - - + +
4970B PRO 3.8 23.3 - - - -
4971B HIS* 3.8 23.8 - + + -
4972B ARG* 1.3 80.7 - - - +
4974B GLU* 1.3 87.6 + - + +
4976B HIS* 3.9 9.4 + - - +
4977B THR* 4.3 6.8 + - - -
4223H SER* 5.1 16.8 - - - -
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Residues in contact with GLU4974 (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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4971B HIS 5.0 0.2 + - - -
4972B ARG 4.9 0.2 - - - +
4973B PHE* 1.3 99.3 - - + +
4975B THR* 1.3 65.0 + - - +
4976B HIS 3.2 3.1 + - - -
4977B THR* 3.5 9.3 + - - +
4978B LEU* 3.3 25.1 + - + +
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Residues in contact with THR4975 (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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4187B ARG* 5.7 0.3 + - - -
4971B HIS 4.0 17.5 + - - -
4972B ARG* 3.9 7.7 + - - -
4973B PHE 3.5 0.4 - - - -
4974B GLU* 1.3 76.4 - - - +
4976B HIS* 1.3 66.5 + - - +
4978B LEU* 3.6 12.0 + - - +
4979B GLU* 3.7 11.1 + - - +
4980B GLU 4.3 4.3 + - - -
5026B PHE* 4.7 18.9 - - - -
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Residues in contact with HIS4976 (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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4959B CYS* 4.4 4.9 - - + -
4961B ILE* 3.4 14.1 - - + +
4962B GLY 4.4 3.1 + - - -
4963B SER 4.7 2.2 - - - -
4964B ASP* 4.4 13.4 - - - -
4965B TYR* 3.7 25.5 - - + +
4972B ARG 3.3 19.4 + - - +
4973B PHE 4.1 6.1 - - - +
4974B GLU 3.2 0.6 - - - -
4975B THR* 1.3 78.5 - - - +
4977B THR* 1.3 61.9 + - - +
4978B LEU 3.2 2.8 + - - -
4981B HIS* 2.6 69.8 + + + +
5025B CYS* 3.7 12.3 - - + +
5026B PHE* 4.8 9.9 - - - -
5101B ZN 2.3 29.8 - - - -
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Residues in contact with THR4977 (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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4973B PHE 4.3 5.3 + - - -
4974B GLU* 3.5 12.1 + - - +
4976B HIS* 1.3 79.3 - - - +
4978B LEU* 1.3 56.4 + - - +
4981B HIS 3.4 13.7 - - - -
4982B ASN* 3.4 20.5 - - - +
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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