Contacts of the helix formed by residues 4986 - 4996 (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 TYR4986 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4175D ARG 3.9 19.9 + - - -
4176D ILE* 4.6 14.3 - - + -
4177D GLU 5.3 1.1 + - - -
4190D PHE* 6.1 2.9 - + - -
4200D TRP* 5.4 0.6 - - - -
4229D PHE* 4.4 24.7 - + + -
4233D CYS* 5.3 1.3 - - - -
4958D ILE* 4.5 13.8 + - + -
4959D CYS* 5.6 1.0 + - - -
4980D GLU 3.7 19.1 + - - -
4981D HIS* 4.5 2.8 - - - -
4982D ASN* 4.3 4.4 + - + -
4983D LEU* 3.7 37.1 + - - -
4984D ALA* 3.0 13.9 - - - +
4985D ASN* 1.3 76.7 - - - +
4987D MET* 1.3 63.9 + - - +
4988D PHE 3.1 1.3 - - - -
4989D PHE* 3.1 27.9 + + + +
4990D LEU* 3.4 15.1 + - + +
5020D PHE* 4.4 23.1 - + + -
5021D PRO* 5.9 5.7 - - + +
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Residues in contact with MET4987 (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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4196D ASN* 4.4 4.2 + - - +
4200D TRP* 4.3 23.9 - - + -
4229D PHE* 5.8 0.4 - - - -
4233D CYS* 4.3 27.8 - - + -
4236D THR* 4.4 13.5 - - + +
4237D ILE* 4.5 10.5 - - + +
4985D ASN 3.2 0.6 - - - -
4986D TYR* 1.3 79.3 - - - +
4988D PHE* 1.3 56.4 + - - +
4990D LEU* 3.4 4.7 + - - +
4991D MET* 2.9 27.8 + - - +
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Residues in contact with PHE4988 (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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4190D PHE* 4.5 5.6 - - + -
4192D ILE* 4.2 28.0 - - + -
4196D ASN* 3.2 27.8 + - + +
4200D TRP* 6.1 0.4 - - - -
4985D ASN* 3.2 17.0 + - + +
4986D TYR 3.1 0.8 - - - -
4987D MET* 1.3 76.2 - - - +
4989D PHE* 1.3 60.0 + - - +
4991D MET* 3.5 7.1 - - - +
4992D TYR* 2.9 27.9 + - - +
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Residues in contact with PHE4989 (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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4176D ILE* 4.7 12.6 - - + -
4178D ILE* 5.0 12.6 - - + -
4188D ILE* 4.7 12.6 - - + -
4190D PHE* 3.5 45.8 - + + -
4985D ASN 4.0 1.2 + - - -
4986D TYR* 3.1 21.7 + + + +
4988D PHE* 1.3 79.6 - - - +
4990D LEU* 1.3 74.4 + - + +
4992D TYR* 3.2 14.6 + + + +
4993D LEU* 3.2 35.7 + - + +
5004D GLN 5.4 0.9 - - - -
5005D GLU* 5.2 6.1 - - + -
5008D VAL* 3.8 41.5 - - + -
5019D PHE* 5.7 4.0 - + - -
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Residues in contact with LEU4990 (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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4229D PHE* 6.2 1.6 - - + -
4230D VAL* 4.5 12.3 - - + +
4233D CYS* 4.5 23.6 - - + -
4234D GLU* 5.7 2.2 - - + +
4237D ILE* 6.4 0.2 - - - -
4714D TRP* 6.1 4.9 - - + -
4986D TYR* 3.4 17.1 + - + +
4987D MET* 3.4 8.9 + - - +
4989D PHE* 1.3 89.7 - - + +
4991D MET* 1.3 65.5 + - - +
4993D LEU* 3.3 7.4 + - - +
4994D ILE* 3.1 30.9 + - + +
5012D TYR* 4.2 31.0 - - + +
5019D PHE* 5.1 15.9 - - + -
5020D PHE* 6.4 0.9 - - + -
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Residues in contact with MET4991 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4193D SER* 5.2 4.7 - - - +
4195D THR* 6.0 5.6 - - + -
4196D ASN* 3.6 34.3 - - + +
4237D ILE* 3.7 39.4 - - + +
4987D MET 2.9 18.5 + - - +
4988D PHE 3.5 6.1 - - - +
4989D PHE 3.2 0.4 - - - -
4990D LEU* 1.3 77.1 - - - +
4992D TYR* 1.3 56.3 + - - +
4994D ILE* 4.5 8.1 - - - +
4995D ASN* 2.8 43.9 + - + +
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Residues in contact with TYR4992 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4190D PHE* 4.9 21.8 - + + -
4191D GLU* 4.1 26.9 - - + +
4988D PHE 2.9 13.8 + - - +
4989D PHE* 3.2 14.1 + + + +
4991D MET* 1.3 77.9 - - - +
4993D LEU* 1.3 72.2 + - + +
4995D ASN* 4.8 3.1 - - + -
4996D LYS* 3.1 41.9 + - + +
5000D GLU* 3.7 21.2 + - - +
5001D HIS* 5.5 2.0 - - + -
5002D THR* 6.1 1.3 - - + -
5005D GLU* 4.8 14.6 - - + -
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Residues in contact with LEU4993 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4989D PHE* 3.2 40.8 - - + +
4990D LEU* 3.3 11.3 + - - +
4991D MET 3.3 0.4 - - - -
4992D TYR* 1.3 91.7 - - + +
4994D ILE* 1.3 60.6 + - - +
4996D LYS* 3.0 17.3 - - - +
4997D ASP 5.3 0.3 - - - -
5001D HIS* 5.0 7.2 - - + -
5005D GLU* 3.4 35.7 - - + +
5008D VAL* 4.7 4.3 - - + -
5009D TRP* 3.7 46.0 - - + -
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Residues in contact with ILE4994 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3748D PHE* 5.6 17.7 - - + -
4237D ILE* 5.9 5.8 - - + -
4714D TRP* 4.5 34.3 - - + -
4990D LEU* 3.1 20.0 + - + +
4991D MET* 3.9 10.5 - - - +
4993D LEU* 1.3 78.0 - - - +
4995D ASN* 1.3 66.8 + - - +
4996D LYS 3.8 2.6 - - - +
4997D ASP* 5.6 0.3 - - - +
5009D TRP* 3.7 29.6 - - + -
5012D TYR* 5.5 6.1 - - + -
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Residues in contact with ASN4995 (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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4991D MET* 2.8 34.8 + - + +
4992D TYR* 4.5 2.7 - - - +
4994D ILE* 1.3 78.0 - - - +
4996D LYS* 1.3 63.1 + - - +
4997D ASP* 3.7 7.8 + - - +
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Residues in contact with LYS4996 (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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4992D TYR* 3.1 37.5 + - + +
4993D LEU* 3.0 21.9 - - - +
4994D ILE 3.8 2.8 - - - +
4995D ASN* 1.3 82.6 - - - +
4997D ASP* 1.3 69.2 + - - +
5000D GLU* 4.4 14.8 - - + +
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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