Contacts of the helix formed by residues 252 - 260 (chain A) in PDB entry 4OWW
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 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A GLY* 1.3 70.5 - - - -
253A ASP* 1.3 63.4 + - - +
254A LEU 3.1 0.2 - - - -
255A VAL* 2.9 28.4 + - - +
291A LEU* 3.4 16.5 + - - +
292A LEU* 2.8 36.8 + - + +
293A GLN* 3.7 18.4 + - - +
294A SER 2.9 13.1 + - - +
295A ARG* 3.4 20.3 - - - +
296A THR* 3.5 7.9 + - - +
397A TYR* 3.5 39.5 + - + -
398A ASP* 2.9 33.5 + - - +
401A PHE* 4.3 12.0 + - - +
407A ASP* 3.0 38.7 + - - -
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Residues in contact with ASP 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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210A TYR* 3.9 15.9 - - + +
250A ILE* 4.5 1.1 - - + -
252A ARG* 1.3 77.4 - - - +
254A LEU* 1.3 66.1 + - - +
256A ARG* 2.9 40.5 + - - +
257A LEU* 2.9 26.3 + - - +
296A THR* 2.9 34.0 + - + +
301A LEU* 3.7 9.7 - - - +
351A ARG* 2.8 36.9 + - - -
397A TYR* 4.7 2.5 - - - -
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Residues in contact with LEU 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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209A VAL* 4.7 0.4 - - + -
213A LEU* 3.6 27.4 - - + -
240A LEU* 4.5 11.9 - - + -
244A PHE* 4.8 4.5 - - + -
247A CYS* 3.6 33.4 - - + +
248A LEU* 4.5 5.6 - - + +
250A ILE* 3.7 30.2 - - + +
251A GLY 3.0 14.3 + - - +
253A ASP* 1.3 78.2 - - - +
255A VAL* 1.3 56.5 + - - +
257A LEU* 3.4 5.4 + - + +
258A LEU* 2.9 50.4 + - + +
291A LEU* 4.0 20.9 - - + -
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Residues in contact with VAL 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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252A ARG 2.9 14.3 + - - +
254A LEU* 1.3 76.5 - - - +
256A ARG* 1.3 56.3 + - - +
258A LEU* 3.2 9.2 + - + +
259A GLN* 2.8 28.9 + - - +
271A TRP* 3.9 10.5 - - + -
288A ILE* 4.1 17.0 - - + -
291A LEU* 3.7 31.4 - - + -
292A LEU* 3.9 20.9 - - + -
397A TYR* 3.4 13.5 - - - +
98C LEU* 3.7 24.7 - - + -
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Residues in contact with ARG 256 (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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210A TYR* 3.4 18.2 + - - -
214A ARG* 6.0 1.4 - - - +
252A ARG 3.6 1.0 + - - -
253A ASP* 2.9 38.0 + - - +
255A VAL* 1.3 75.3 - - - +
257A LEU* 1.3 74.7 + - - +
259A GLN* 3.2 10.8 - - + +
260A ASN* 3.1 48.7 + - - +
347A CYS* 4.2 19.0 + - - +
348A ASP* 4.9 11.3 + - - +
351A ARG* 3.5 30.2 - - - +
390A ASN 5.7 0.9 - - - -
393A LEU* 5.2 3.6 - - + -
394A ALA* 4.4 11.2 - - - +
397A TYR* 3.1 43.5 + - + -
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Residues in contact with LEU 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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210A TYR* 3.4 63.5 - - + +
213A LEU* 4.1 22.8 - - + +
214A ARG* 4.2 27.1 - - + -
217A VAL* 5.7 0.6 - - + +
253A ASP 2.9 15.5 + - - +
254A LEU* 3.6 8.7 - - + +
256A ARG* 1.3 98.1 - - - +
258A LEU* 1.3 63.1 + - - +
260A ASN* 3.3 19.6 + - - +
261A VAL* 3.6 17.4 + - - +
348A ASP* 5.6 0.9 - - - +
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Residues in contact with LEU 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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213A LEU* 3.8 19.5 - - + -
240A LEU* 4.1 12.6 - - + -
244A PHE* 5.3 2.5 - - + -
254A LEU* 2.9 43.2 + - + +
255A VAL* 3.2 4.7 + - + +
257A LEU* 1.3 76.9 - - - +
259A GLN* 1.3 61.5 + - - +
261A VAL* 3.3 7.5 + - - +
262A ALA 3.2 12.6 + - - -
267A PHE* 3.9 29.8 - - + -
270A LEU* 4.4 5.8 - - + -
271A TRP* 2.9 32.6 + - + +
274A ILE* 3.7 26.5 - - + -
291A LEU* 5.7 2.5 - - + -
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Residues in contact with GLN 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 VAL 2.8 11.8 + - - +
256A ARG* 3.2 17.7 - - - +
258A LEU* 1.3 77.6 - - - +
260A ASN* 1.3 66.8 + - - +
261A VAL 3.4 0.5 + - - -
262A ALA* 3.5 7.2 - - - +
271A TRP* 3.7 16.3 - - + +
393A LEU* 3.4 23.7 - - - +
397A TYR* 3.0 36.4 + - - -
444A PHE* 3.7 5.1 - - - -
81C GLY* 3.3 0.7 - - - -
82C TYR 3.2 27.0 + - - -
96C PRO* 3.7 5.8 + - + +
97C VAL* 3.6 36.7 + - - +
98C LEU* 3.9 11.7 - - + +
99C PRO* 5.0 0.9 - - + -
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Residues in contact with ASN 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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214A ARG* 6.2 2.0 - - - +
217A VAL* 4.3 23.5 - - + +
256A ARG* 3.1 42.0 + - - +
257A LEU* 3.7 12.4 - - - +
258A LEU 3.2 0.6 - - - -
259A GLN* 1.3 87.2 - - - +
261A VAL* 1.3 59.8 + - - +
262A ALA 3.5 0.4 - - - -
347A CYS* 6.0 2.8 - - - +
390A ASN* 3.9 27.8 + - - +
393A LEU* 5.8 1.0 - - - +
79C SER* 5.0 0.3 + - - -
80C SER* 3.2 7.6 + - - -
81C GLY* 3.2 23.8 + - - -
96C PRO* 5.7 0.9 - - - +
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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