Contacts of the helix formed by residues 251 - 261 (chain A) in PDB entry 2OQH
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 ARG 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PHE* 5.8 6.3 - - - +
94A TYR* 3.7 31.4 + - + +
249A VAL* 4.5 0.2 - - - +
250A VAL* 1.3 85.9 - - + +
252A PHE* 1.3 58.8 + - - +
253A GLU* 3.7 40.1 + - - +
254A ASP* 2.8 51.2 + - - +
255A PHE 3.6 2.1 + - - -
274A TRP* 3.4 18.0 - - - +
247C MSE 5.0 9.7 + - - -
248C CYS* 5.4 6.7 + - - +
250C VAL* 5.9 4.0 - - - +
251C ARG* 5.9 3.2 - - - +
254C ASP* 5.1 12.1 + - - -
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Residues in contact with PHE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ARG* 1.3 72.6 - - - +
253A GLU* 1.3 67.3 + - - +
255A PHE* 2.9 25.0 + + + +
256A ALA* 4.1 3.3 + - - +
274A TRP* 3.4 28.7 - + - -
279A ALA* 3.4 38.1 - - + -
282A ALA* 3.8 12.8 - - + -
283A LEU* 3.8 9.4 - - + -
286A HIS* 3.7 44.6 - + - -
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Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 4.3 6.6 + - - -
251A ARG* 3.1 51.7 + - - +
252A PHE* 1.3 78.7 + - - +
254A ASP* 1.3 59.2 + - - +
256A ALA* 6.1 0.2 - - - -
257A PRO* 3.5 20.7 - - - +
227C VAL* 5.2 11.4 - - + +
228C GLY* 4.8 22.3 - - - +
229C ILE* 4.9 8.0 + - - +
230C GLU* 5.5 0.3 + - - +
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Residues in contact with ASP 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 4.0 8.4 - - + +
248A CYS 3.6 14.5 - - - +
249A VAL* 3.7 16.4 - - - -
250A VAL* 3.1 26.0 + - - +
251A ARG* 2.8 42.1 + - - +
253A GLU* 1.3 80.8 - - - +
255A PHE* 1.3 63.0 + - - +
257A PRO* 3.4 5.8 - - - +
258A ALA* 3.1 25.2 + - - +
251C ARG* 4.9 11.7 + - - -
254C ASP* 5.3 2.4 - - - +
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Residues in contact with PHE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A VAL* 4.4 10.7 - - + +
251A ARG 3.6 1.8 + - - +
252A PHE* 2.9 26.6 + + + +
254A ASP* 1.3 74.8 - - - +
256A ALA* 1.3 69.8 + - - +
258A ALA* 3.1 4.9 + - - +
259A MSE 2.9 55.8 + - + +
267A ILE* 3.5 31.6 - - + -
274A TRP* 5.4 1.1 - + + -
283A LEU* 4.2 12.8 - - + -
286A HIS* 3.6 51.4 - + + -
287A CYS 4.9 0.7 - - - -
290A PHE* 3.5 21.1 - + - -
292A LEU* 4.0 6.5 - - + -
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Residues in contact with ALA 256 (chain A).
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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252A PHE 4.1 3.1 + - - +
253A GLU 5.5 0.2 - - - +
255A PHE* 1.3 80.3 - - - +
257A PRO* 1.3 74.1 - - + +
259A MSE 3.1 6.8 + - - +
260A ARG* 2.9 26.7 + - + +
230C GLU* 3.4 37.5 - - + +
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Residues in contact with PRO 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 4.4 12.3 - - + -
253A GLU 3.5 20.0 - - - +
254A ASP* 3.4 12.6 - - - +
256A ALA* 1.3 94.8 - - + +
258A ALA* 1.3 61.5 + - - +
260A ARG* 3.3 1.7 + - + +
261A LEU* 3.0 30.7 + - - +
229C ILE* 3.9 28.5 - - + -
230C GLU* 4.2 8.0 - - + +
257C PRO* 4.9 7.0 - - + -
261C LEU* 3.6 25.4 - - + -
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Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 4.1 16.9 - - + +
249A VAL* 3.5 26.7 - - + -
254A ASP 3.1 20.5 + - - +
255A PHE* 3.1 4.9 + - - +
257A PRO* 1.3 76.4 - - - +
259A MSE 1.3 70.2 + - + +
261A LEU 3.7 0.2 - - - -
262A ASN* 3.0 7.1 + - - -
263A ALA* 3.0 35.3 + - + -
264A VAL* 5.0 0.7 - - + -
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Residues in contact with MSE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A PHE* 2.9 40.1 + - + +
256A ALA* 3.6 7.6 - - - +
258A ALA* 1.3 87.4 - - + +
260A ARG* 1.3 65.9 + - + +
262A ASN* 3.1 22.8 + - - +
263A ALA 5.6 0.2 - - - +
264A VAL* 3.8 24.9 - - + +
267A ILE* 4.7 2.5 - - + -
290A PHE* 3.8 39.3 - - + -
292A LEU* 3.6 39.9 - - + -
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Residues in contact with ARG 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ALA* 2.9 18.6 + - - +
257A PRO 3.9 1.6 - - - +
259A MSE 1.3 77.7 - - + +
261A LEU* 1.3 61.7 + - - +
262A ASN* 3.3 9.6 + - - -
230C GLU* 2.6 41.4 + - - -
234C GLN* 3.7 12.5 - - - +
261C LEU* 3.8 29.1 - - + +
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 3.7 29.8 - - + -
230A GLU* 5.1 4.7 - - - +
233A ALA* 3.3 18.9 - - + +
257A PRO 3.0 17.3 + - - +
258A ALA 4.3 0.4 - - - +
260A ARG* 1.3 77.9 - - - +
262A ASN* 1.3 73.4 + - - +
263A ALA 3.3 1.0 + - - -
257C PRO* 3.7 32.5 - - + +
260C ARG* 3.9 30.7 - - + -
261C LEU* 3.8 24.2 - - + -
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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