Contacts of the helix formed by residues 234 - 244 (chain R) in PDB entry 6GYK
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 HIS 234 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118R HIS* 5.5 1.3 - - - -
226R PRO* 6.1 5.8 - - + -
233R TYR* 1.3 76.7 - - - +
235R LYS* 1.3 59.0 + - - +
236R ILE 3.2 0.2 - - - -
237R VAL* 3.2 10.9 + - + +
238R GLU* 2.9 27.9 + - - +
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Residues in contact with LYS 235 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233R TYR* 3.2 2.5 - - - -
234R HIS* 1.3 78.1 - - - +
236R ILE* 1.3 57.2 + - - +
238R GLU* 3.7 7.6 - - - +
239R GLN* 2.9 28.9 + - - +
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Residues in contact with ILE 236 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233R TYR* 3.4 14.7 + - + +
234R HIS 3.2 0.8 - - - -
235R LYS* 1.3 78.1 - - - +
237R VAL* 1.3 57.0 + - - +
239R GLN* 3.7 6.4 - - - +
240R ARG* 2.9 28.6 + - - +
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Residues in contact with VAL 237 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76R PHE* 5.4 15.3 - - + -
226R PRO* 6.4 2.2 - - + -
233R TYR 3.9 2.1 + - - +
234R HIS* 3.2 17.4 + - + +
236R ILE* 1.3 75.6 - - - +
238R GLU* 1.3 60.7 + - - +
240R ARG* 3.3 7.1 + - - +
241R ARG* 2.9 27.9 + - - +
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Residues in contact with GLU 238 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561B TRP* 5.9 9.6 - - + -
234R HIS 2.9 16.3 + - - +
235R LYS* 3.7 8.5 - - - +
237R VAL* 1.3 77.2 - - - +
239R GLN* 1.3 57.9 + - - +
241R ARG* 3.3 7.5 + - - +
242R ASN* 2.9 27.2 + - - +
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Residues in contact with GLN 239 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235R LYS 2.9 18.1 + - - +
236R ILE* 3.7 7.6 - - - +
237R VAL 3.3 0.2 - - - -
238R GLU* 1.3 74.2 - - - +
240R ARG* 1.3 59.3 + - - +
242R ASN* 3.3 8.2 + - - +
243R ILE* 2.8 29.8 + - - +
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Residues in contact with ARG 240 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236R ILE 2.9 17.8 + - - +
237R VAL* 3.7 8.1 - - - +
238R GLU 3.3 0.2 - - - -
239R GLN* 1.3 76.6 - - - +
241R ARG* 1.3 57.4 + - - +
243R ILE* 3.5 8.0 - - - +
244R VAL* 3.0 28.4 + - - +
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Residues in contact with ARG 241 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B PHE* 4.1 28.5 - - + -
560B GLU* 3.6 25.6 - - - +
561B TRP* 5.9 3.8 - - + -
237R VAL 2.9 17.2 + - - +
238R GLU* 3.6 8.3 - - - +
239R GLN 3.3 0.2 - - - -
240R ARG* 1.3 76.5 - - - +
242R ASN* 1.3 62.7 + - - +
243R ILE 3.5 0.2 + - - -
244R VAL* 3.7 14.2 + - - +
245R LYS* 4.2 5.0 + - - +
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Residues in contact with ASN 242 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B PHE* 4.9 4.2 - - + -
603B LEU* 5.9 7.0 - - + -
608B ASP* 5.2 14.3 - - - +
238R GLU 2.9 16.4 + - - +
239R GLN* 3.3 8.7 + - - +
241R ARG* 1.3 76.2 - - - +
243R ILE* 1.3 60.2 + - - +
245R LYS* 3.4 19.9 + - - +
246R LEU* 5.3 0.7 - - - +
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Residues in contact with ILE 243 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239R GLN 2.8 18.6 + - - +
240R ARG* 3.1 10.9 + - - +
242R ASN* 1.3 75.3 - - - +
244R VAL* 1.3 62.5 + - - +
245R LYS 3.1 3.3 + - - -
246R LEU* 3.5 20.4 + - - +
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Residues in contact with VAL 244 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B PRO* 5.1 5.8 - - - +
556B THR* 6.4 2.2 - - + -
560B GLU* 5.8 3.1 - - - +
240R ARG 3.0 14.7 + - - +
241R ARG* 4.1 8.5 - - - +
242R ASN 3.4 0.2 - - - -
243R ILE* 1.3 77.8 - - - +
245R LYS* 1.3 55.5 + - - +
246R LEU 3.2 5.9 + - - -
247R ASN* 4.2 10.7 + - - +
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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