Contacts of the helix formed by residues 254 - 263 (chain A) in PDB entry 6O81
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 PRO 254 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ASP* 4.5 0.2 - - - +
144A VAL* 3.9 23.1 - - + +
145A ARG 3.5 21.5 - - - +
146A SER* 3.9 3.1 - - - -
147A ASP* 3.5 22.4 - - - +
148A PHE* 3.7 13.5 - - + -
172A ARG* 5.7 3.6 - - - +
253A SER* 1.3 85.9 - - - +
255A GLN* 1.3 63.3 + - + +
256A VAL 3.2 0.9 - - - -
257A ALA* 3.3 18.8 + - + +
258A GLN* 3.7 13.4 + - - +
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Residues in contact with GLN 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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172A ARG* 3.2 36.3 - - - +
177A ASN* 3.6 23.0 + - - +
180A VAL* 3.8 19.6 - - + +
253A SER* 3.1 6.5 - - - -
254A PRO* 1.3 79.9 - - + +
256A VAL* 1.3 61.3 + - - +
257A ALA 3.2 0.4 - - - -
258A GLN* 3.2 16.4 + - + +
259A LEU* 2.9 32.2 + - + +
285A ASN* 4.2 13.6 + - - +
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 4.5 11.7 - - + -
148A PHE* 4.1 9.4 - - + -
150A LEU* 6.0 0.2 - - + -
180A VAL* 3.7 22.0 - - + +
181A MET* 3.8 26.9 - - + -
252A CYS* 3.6 22.4 - - + -
253A SER 3.3 16.8 - - - +
255A GLN* 1.3 76.4 - - - +
257A ALA* 1.3 60.4 + - - +
259A LEU* 3.4 7.8 + - + +
260A PHE* 2.9 38.5 + - + -
272A PHE* 4.0 18.4 - - + -
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Residues in contact with ALA 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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135A LEU* 3.5 32.0 - - + +
138A VAL* 4.9 8.3 - - + -
139A ASP* 3.7 20.1 - - + +
144A VAL* 5.9 1.8 - - + -
148A PHE* 5.4 2.5 - - + -
254A PRO* 3.3 13.3 + - + +
255A GLN 3.2 0.4 - - - -
256A VAL* 1.3 81.0 - - + +
258A GLN* 1.3 58.2 + - - +
260A PHE* 3.3 5.3 + - - +
261A THR* 2.9 33.4 + - - +
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Residues in contact with GLN 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP* 2.8 23.9 + - - +
254A PRO* 3.7 16.2 + - - +
255A GLN* 3.2 16.3 + - + +
257A ALA* 1.3 77.7 - - - +
259A LEU* 1.3 58.1 + - + +
261A THR* 2.6 22.8 + - - +
262A ASP* 2.9 23.0 + - - +
75T ARG* 2.8 39.1 + - + +
350T ALA 5.1 0.3 - - - +
352T ARG* 3.7 16.6 - - - +
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Residues in contact with LEU 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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180A VAL* 5.2 5.2 - - + -
255A GLN* 2.9 23.0 + - + +
256A VAL* 3.8 5.8 - - - +
257A ALA 3.3 0.2 - - - -
258A GLN* 1.3 77.7 - - + +
260A PHE* 1.3 58.7 + - - +
262A ASP* 3.9 14.4 - - + +
263A ASN* 3.0 38.7 + - - +
266A TYR* 4.5 3.2 - - + -
272A PHE* 4.1 27.6 - - + -
276A LEU* 4.4 12.3 - - + -
283A LEU* 4.0 31.2 - - + -
285A ASN* 3.7 25.8 - - + +
75T ARG 5.5 1.3 - - - +
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Residues in contact with PHE 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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131A LEU* 4.6 4.0 - - + -
132A GLY* 3.6 32.1 - - - +
135A LEU* 3.6 31.9 - - + -
136A ARG* 2.5 35.8 + - - +
181A MET* 6.1 0.9 - - + -
256A VAL* 2.9 26.9 + - + +
257A ALA* 3.7 7.0 - - - +
258A GLN 3.2 0.4 - - - -
259A LEU* 1.3 76.2 - - - +
261A THR* 1.3 60.2 + - - +
263A ASN 3.0 9.2 - - - +
264A PHE* 4.3 0.2 - - - -
266A TYR* 3.3 39.5 - + + -
268A THR 3.4 25.4 - - - -
269A ARG* 5.0 1.1 - - - -
272A PHE* 3.6 30.1 - + + -
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Residues in contact with THR 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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136A ARG* 3.8 24.5 - - + +
139A ASP* 3.5 26.0 - - + +
140A ALA 5.5 0.2 - - - +
257A ALA 2.9 16.6 + - - +
258A GLN* 2.6 23.0 + - - -
260A PHE* 1.3 76.1 - - - +
262A ASP* 1.3 61.9 + - - +
264A PHE* 3.2 27.6 - - - -
75T ARG* 2.6 27.2 + - - +
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Residues in contact with ASP 262 (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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258A GLN* 2.9 18.8 + - - +
259A LEU* 3.6 16.3 + - + +
260A PHE 3.3 0.2 - - - -
261A THR* 1.3 80.9 - - - +
263A ASN* 1.3 71.8 + - - +
264A PHE* 3.4 13.7 + - - -
283A LEU* 5.8 2.6 - - + +
75T ARG* 2.8 60.0 + - - +
76T ASN* 4.9 8.8 - - + +
405T MET* 4.8 5.2 - - - +
451T TRP* 5.4 1.6 + - - -
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Residues in contact with ASN 263 (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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136A ARG* 3.5 3.1 + - - -
259A LEU* 3.0 23.4 + - - +
260A PHE* 3.0 19.0 - - - +
262A ASP* 1.3 81.8 + - - +
264A PHE* 1.3 63.3 + - - +
265A ASP* 3.3 16.3 + - - +
266A TYR* 3.3 42.2 + - + +
283A LEU* 4.9 16.6 - - - +
446T ARG* 3.2 22.6 - - - +
451T TRP* 4.8 4.4 - - - +
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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