Contacts of the helix formed by residues 230 - 241 (chain F) in PDB entry 2NQB
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 THR 230 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663E ARG* 5.7 4.1 - - + +
227F GLN 4.1 6.3 - - - +
228F GLY* 2.9 17.6 + - - +
229F ILE* 1.3 72.7 - - - +
231F LYS* 1.3 65.9 + - - +
232F PRO* 3.2 14.0 - - - +
233F ALA* 3.2 23.9 + - - +
234F ILE* 3.0 25.8 + - - +
255F ARG* 3.9 4.0 - - - +
207J A 3.8 34.6 + - - +
208J T 3.5 13.7 - - - +
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Residues in contact with LYS 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F THR* 1.3 71.9 - - - +
232F PRO* 1.3 68.4 - - + +
234F ILE* 3.2 3.3 + - - +
235F ARG* 2.9 45.9 + - + +
251F TYR* 3.5 54.9 - - + -
255F ARG* 3.7 9.7 - - - +
81I G 5.5 4.2 + - - -
208J T 4.3 4.1 + - - +
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Residues in contact with PRO 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F THR* 3.2 16.4 - - - +
231F LYS* 1.3 96.4 - - + +
233F ALA* 1.3 63.7 + - - +
235F ARG* 3.3 10.5 + - + +
236F ARG* 3.0 33.8 + - - +
207J A 3.7 34.5 - - + +
208J T 3.7 26.2 - - + +
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Residues in contact with ALA 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661E LEU 3.7 16.0 - - - +
662E ILE* 4.1 21.3 - - + -
663E ARG* 5.0 2.0 - - + +
228F GLY 5.5 0.7 - - - +
229F ILE* 4.8 2.7 - - + -
230F THR* 3.2 26.4 + - - +
232F PRO* 1.3 78.8 - - - +
234F ILE* 1.3 63.3 + - - +
236F ARG* 3.3 19.3 + - - +
237F LEU* 3.1 27.8 + - - +
207J A 5.1 0.2 - - - +
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Residues in contact with ILE 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704E PHE* 3.8 23.0 - - + -
229F ILE* 3.8 31.2 - - + +
230F THR 3.0 15.4 + - - +
231F LYS 3.6 6.5 - - - +
233F ALA* 1.3 74.5 - - - +
235F ARG* 1.3 64.9 - - - +
237F LEU* 3.3 10.1 + - + +
238F ALA* 3.0 21.7 + - + +
246F ILE* 6.0 0.4 - - + -
250F ILE* 4.6 3.8 - - + -
251F TYR* 3.6 50.3 - - + +
254F THR* 4.0 20.4 - - + +
255F ARG* 4.2 6.1 - - + +
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Residues in contact with ARG 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650E GLU* 5.1 6.0 + - - +
231F LYS* 2.9 43.9 + - + +
232F PRO* 3.5 9.2 - - + +
234F ILE* 1.3 75.7 - - - +
236F ARG* 1.3 59.6 + - + +
238F ALA* 3.1 4.3 + - - +
239F ARG* 2.8 59.0 + - + +
246F ILE* 3.8 19.1 - - + +
251F TYR* 3.0 27.1 + - + -
81I G 2.6 62.2 + - - +
82I A 4.5 5.9 + - - -
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Residues in contact with ARG 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654E TYR* 3.5 41.3 - - + +
661E LEU* 2.8 56.0 + - + +
663E ARG* 4.8 8.9 - - - +
232F PRO* 3.0 25.2 + - - +
233F ALA* 3.5 22.2 - - - +
234F ILE 3.3 0.2 - - - -
235F ARG* 1.3 77.8 - - + +
237F LEU* 1.3 61.7 + - - +
239F ARG* 3.1 10.8 + - - +
240F ARG* 3.0 19.2 + - - +
206J C 4.9 2.9 - - - -
207J A 2.7 43.6 + - - -
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Residues in contact with LEU 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661E LEU* 3.9 15.9 - - + +
662E ILE* 4.0 18.4 - - + -
697E GLU* 3.8 36.1 - - + +
700E LEU* 3.6 30.3 - - + -
701E VAL* 3.8 27.9 - - + +
704E PHE* 3.9 15.9 - - + -
229F ILE* 5.5 0.2 - - + -
233F ALA 3.1 19.0 + - - +
234F ILE* 3.6 16.6 - - + +
235F ARG 3.3 0.2 - - - -
236F ARG* 1.3 75.2 - - - +
238F ALA* 1.3 63.5 + - - +
240F ARG* 3.4 4.0 + - - +
241F GLY* 3.1 17.5 + - - -
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Residues in contact with ALA 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704E PHE* 3.6 29.5 - - + -
234F ILE* 3.0 13.0 + - + +
235F ARG 3.4 8.3 - - - +
237F LEU* 1.3 74.1 - - - +
239F ARG* 1.3 64.6 + - - +
241F GLY* 3.0 8.5 + - - -
242F GLY 3.1 0.3 + - - -
243F VAL* 2.8 39.3 + - + +
246F ILE* 3.9 21.5 - - + -
250F ILE* 6.2 0.2 - - + -
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Residues in contact with ARG 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647E ALA* 3.6 28.7 + - - +
650E GLU* 2.8 48.5 + - + +
651E ILE* 3.7 18.5 - - - +
654E TYR* 3.8 17.9 - - + -
655E GLN* 4.0 0.2 - - - +
235F ARG* 2.8 54.8 + - + +
236F ARG* 3.1 8.5 + - - +
238F ALA* 1.3 76.3 - - - +
240F ARG* 1.3 54.9 + - - +
242F GLY* 2.7 24.8 + - - -
243F VAL 2.8 34.3 + - - -
244F LYS* 3.3 17.4 + - - +
246F ILE* 4.1 18.2 - - - +
81I G 4.8 3.2 + - - -
82I A 4.6 3.0 + - - -
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Residues in contact with ARG 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906C GLY* 4.9 7.7 - - - -
907C VAL* 3.6 30.2 - - + +
654E TYR* 2.8 22.9 + - + +
655E GLN* 3.3 25.6 + - - +
657E SER* 3.1 28.4 + - - -
658E THR* 4.0 7.9 + - - +
659E GLU* 3.0 45.9 + - - -
661E LEU* 3.6 26.5 - - + +
697E GLU* 4.6 5.5 + - - +
701E VAL* 3.9 23.1 - - + +
705E GLU* 4.8 1.2 - - - +
236F ARG 3.0 12.4 + - - +
237F LEU 3.7 7.9 - - - +
239F ARG* 1.3 76.6 - - - +
241F GLY* 1.3 56.6 + - - +
242F GLY 3.1 0.2 - - - -
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Residues in contact with GLY 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655E GLN* 4.3 2.5 - - - -
701E VAL* 3.9 11.0 - - - +
704E PHE* 4.2 5.9 - - - +
705E GLU* 3.5 42.0 - - - +
708E ASN* 4.4 3.1 + - - -
237F LEU 3.1 10.8 + - - -
238F ALA 3.0 9.5 + - - -
239F ARG 3.0 1.2 - - - -
240F ARG* 1.3 75.5 - - - +
242F GLY* 1.3 60.8 + - - +
243F VAL* 3.4 1.9 + - - +
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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