Contacts of the helix formed by residues 4986 - 4996 (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 TYR4986 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4175B ARG 3.9 20.4 + - - -
4176B ILE* 4.6 15.0 - - + -
4177B GLU 5.3 0.9 + - - -
4190B PHE* 6.1 2.9 - + - -
4200B TRP* 5.4 0.8 - - - -
4229B PHE* 4.4 25.5 - + + -
4233B CYS* 5.3 1.3 - - - -
4958B ILE* 4.5 14.7 + - + -
4959B CYS* 5.6 1.0 + - - -
4980B GLU 3.7 19.2 + - - -
4981B HIS* 4.5 2.4 - - - -
4982B ASN* 4.3 3.4 + - + +
4983B LEU* 3.7 35.8 + - - -
4984B ALA 3.0 14.4 - - - -
4985B ASN* 1.3 76.6 - - - +
4987B MET* 1.3 65.0 + - - +
4988B PHE 3.1 1.1 - - - -
4989B PHE* 3.1 27.8 + - + +
4990B LEU* 3.4 15.1 + - + +
5020B PHE* 4.4 22.7 - + + -
5021B PRO* 5.9 5.3 - - + +
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Residues in contact with MET4987 (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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4196B ASN* 4.4 5.1 + - - +
4200B TRP* 4.3 23.0 - - + -
4229B PHE* 5.8 0.2 - - - -
4233B CYS* 4.3 28.4 - - + -
4236B THR* 4.4 13.5 - - + +
4237B ILE* 4.5 10.9 - - + +
4985B ASN 3.2 0.6 - - - -
4986B TYR* 1.3 78.9 - - - +
4988B PHE* 1.3 56.0 + - - +
4990B LEU* 3.4 5.8 + - - +
4991B MET* 2.9 27.6 + - - +
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Residues in contact with PHE4988 (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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4190B PHE* 4.5 5.5 - - + -
4192B ILE* 4.2 28.5 - - + -
4193B SER 6.0 0.2 - - - +
4196B ASN* 3.2 27.8 + - + +
4200B TRP* 6.1 0.4 - - - -
4985B ASN* 3.2 17.2 + - + +
4986B TYR 3.1 0.8 - - - -
4987B MET* 1.3 77.3 - - - +
4989B PHE* 1.3 58.7 + - - +
4991B MET* 3.5 7.0 - - - +
4992B TYR* 2.9 28.2 + - - +
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Residues in contact with PHE4989 (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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4176B ILE* 4.7 12.1 - - + -
4178B ILE* 5.0 12.8 - - + -
4188B ILE* 4.7 13.2 - - + -
4190B PHE* 3.5 45.2 - + + -
4985B ASN 4.0 0.8 + - - -
4986B TYR* 3.1 21.7 + - + +
4988B PHE* 1.3 79.0 - - - +
4990B LEU* 1.3 74.5 + - + +
4992B TYR* 3.2 14.6 + + + +
4993B LEU* 3.2 36.7 - - + +
5004B GLN 5.4 1.1 - - - -
5005B GLU* 5.2 5.6 - - + -
5008B VAL* 3.8 41.5 - - + -
5019B PHE* 5.7 4.5 - + - -
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Residues in contact with LEU4990 (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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4229B PHE* 6.2 1.3 - - + -
4230B VAL* 4.5 12.6 - - + +
4233B CYS* 4.5 24.2 - - + -
4234B GLU* 5.7 2.0 - - + +
4714B TRP* 6.1 5.2 - - + -
4986B TYR* 3.4 17.4 + - + +
4987B MET* 3.9 9.2 - - - +
4988B PHE 3.4 0.2 - - - -
4989B PHE* 1.3 89.7 - - + +
4991B MET* 1.3 64.8 + - - +
4993B LEU* 3.3 7.7 + - - +
4994B ILE* 3.1 30.0 + - + +
5012B TYR* 4.2 31.9 - - + +
5019B PHE* 5.1 15.5 - - + -
5020B PHE* 6.4 0.7 - - + -
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Residues in contact with MET4991 (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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4193B SER* 5.2 4.7 - - - +
4195B THR* 6.0 5.6 - - + -
4196B ASN* 3.6 35.0 - - + +
4237B ILE* 3.7 39.6 - - + +
4987B MET 2.9 18.3 + - - +
4988B PHE 3.5 5.8 - - - +
4989B PHE 3.2 0.2 - - - -
4990B LEU* 1.3 77.9 - - - +
4992B TYR* 1.3 57.6 + - - +
4994B ILE* 4.5 8.1 - - - +
4995B ASN* 2.8 44.1 + - + +
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Residues in contact with TYR4992 (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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4190B PHE* 4.9 21.8 - + + -
4191B GLU* 4.1 26.2 - - + +
4988B PHE 2.9 14.2 + - - +
4989B PHE* 3.2 13.9 + + - +
4991B MET* 1.3 77.9 - - - +
4993B LEU* 1.3 70.7 + - + +
4995B ASN* 4.8 3.1 - - - -
4996B LYS* 3.1 42.3 + - + +
5000B GLU* 3.7 20.7 + - - +
5001B HIS* 5.4 1.3 - - - -
5002B THR* 6.1 1.3 - - + -
5005B GLU* 4.8 15.5 - - + -
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Residues in contact with LEU4993 (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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4989B PHE* 3.2 40.6 - - + +
4990B LEU* 3.3 10.0 + - - +
4991B MET 3.3 0.8 - - - -
4992B TYR* 1.3 91.2 - - + +
4994B ILE* 1.3 60.3 + - + +
4996B LYS* 3.0 17.0 - - - +
4997B ASP 5.3 0.5 - - - -
5001B HIS* 5.0 7.6 - - + -
5005B GLU* 3.4 36.6 - - + +
5008B VAL* 4.7 4.3 - - + -
5009B TRP* 3.7 45.6 - - + -
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Residues in contact with ILE4994 (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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3748B PHE* 5.6 17.7 - - + -
4237B ILE* 5.9 5.8 - - + -
4714B TRP* 4.6 33.4 - - + -
4990B LEU* 3.1 20.7 + - + +
4991B MET* 3.9 11.4 - - - +
4993B LEU* 1.3 77.8 - - - +
4995B ASN* 1.3 66.8 + - - +
4996B LYS 3.8 2.6 - - - +
5009B TRP* 3.7 29.2 - - + -
5012B TYR* 5.5 6.1 - - + -
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Residues in contact with ASN4995 (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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4991B MET* 2.8 35.0 + - + +
4992B TYR* 4.5 2.9 - - + +
4994B ILE* 1.3 76.6 - - - +
4996B LYS* 1.3 62.7 + - - +
4997B ASP* 3.7 8.0 + - - +
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Residues in contact with LYS4996 (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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4992B TYR* 3.1 37.9 + - + +
4993B LEU* 3.0 21.5 - - - +
4994B ILE 3.8 2.6 - - - +
4995B ASN* 1.3 83.0 - - - +
4997B ASP* 1.3 69.6 + - - +
5000B GLU* 4.4 14.1 - - + +
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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