Contacts of the helix formed by residues 4972 - 4977 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4965D TYR* 3.3 37.5 + - + +
4966D PHE 3.9 3.6 - - - -
4969D THR* 3.6 21.1 + - - +
4970D PRO 3.6 0.4 - - - -
4971D HIS* 1.3 76.5 - - - +
4973D PHE* 1.3 63.6 + - - +
4974D GLU 3.5 1.3 - - - -
4975D THR* 3.9 10.3 - - - -
4976D HIS* 3.3 22.9 + - - +
5026D PHE* 5.2 9.0 - - + -
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Residues in contact with PHE4973 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4223B SER* 5.1 15.9 - - - -
4964D ASP* 4.3 14.3 - - + +
4966D PHE* 3.7 23.1 - - + +
4970D PRO 3.8 23.3 - - - -
4971D HIS* 3.8 22.7 - + + -
4972D ARG* 1.3 80.9 - - - +
4974D GLU* 1.3 88.7 + - + +
4976D HIS* 3.9 9.4 + - - +
4977D THR* 4.3 5.7 + - - -
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Residues in contact with GLU4974 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4971D HIS 5.0 0.8 + - - +
4972D ARG* 4.5 0.2 - - - +
4973D PHE* 1.3 99.5 - - + +
4975D THR* 1.3 63.9 + - - +
4976D HIS 3.2 2.8 + - - -
4977D THR* 3.5 8.7 + - - +
4978D LEU* 3.3 24.1 + - + +
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Residues in contact with THR4975 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4187D ARG* 5.7 0.5 + - - -
4971D HIS 4.0 17.8 + - - -
4972D ARG* 3.9 7.4 + - - +
4973D PHE 3.5 0.4 - - - -
4974D GLU* 1.3 76.7 - - - +
4976D HIS* 1.3 66.0 + - - +
4978D LEU* 3.6 11.9 + - - +
4979D GLU* 3.7 12.1 + - - +
4980D GLU 4.3 3.8 + - - -
5026D PHE* 4.7 19.4 - - - -
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Residues in contact with HIS4976 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4959D CYS* 4.4 4.3 - - + -
4961D ILE* 3.4 13.9 - - + +
4962D GLY 4.4 3.3 + - - -
4963D SER 4.7 2.2 - - - -
4964D ASP* 4.4 13.8 - - + -
4965D TYR* 3.7 25.5 - - + +
4972D ARG 3.3 19.7 + - - +
4973D PHE 4.1 5.6 - - - +
4974D GLU 3.2 0.8 - - - -
4975D THR* 1.3 77.7 - - - +
4977D THR* 1.3 60.0 + - - +
4978D LEU 3.1 3.0 + - - -
4980D GLU 4.0 0.2 + - - -
4981D HIS* 2.6 70.1 + + + +
5025D CYS* 3.7 11.1 - - + +
5026D PHE* 4.8 9.7 - - - -
5101D ZN 2.3 29.8 - - - -
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Residues in contact with THR4977 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4973D PHE 4.3 5.5 + - - -
4974D GLU* 3.5 12.6 + - - +
4975D THR 3.5 0.2 - - - -
4976D HIS* 1.3 79.6 - - - +
4978D LEU* 1.3 56.9 + - - +
4981D HIS 3.4 13.2 - - - -
4982D ASN* 3.4 21.1 - - - +
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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