Contacts of the helix formed by residues 252 - 263 (chain A) in PDB entry 1ORB
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 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PHE* 3.6 40.4 - - + +
181A SER* 2.8 25.6 + - - -
212A PHE* 3.5 45.3 - - + +
247A CYS* 3.3 7.6 - - - -
251A VAL* 1.3 73.1 - - - +
253A ALA* 1.3 62.0 + - - +
254A CYS 3.0 0.9 - - - -
255A HIS* 3.1 22.2 + - - +
256A ILE 4.1 0.2 + - - -
297A ACT 2.6 23.4 + - + +
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Residues in contact with ALA 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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181A SER* 3.4 10.9 + - - -
245A ALA* 3.6 8.2 - - + +
246A THR* 3.6 31.4 - - - +
247A CYS* 4.0 4.6 - - + +
250A GLY* 4.4 12.8 - - - -
251A VAL 2.9 1.8 + - - +
252A THR* 1.3 75.0 + - - +
254A CYS* 1.3 55.1 + - - +
255A HIS 2.9 5.4 - - - -
256A ILE* 2.7 30.8 + - - +
257A ALA 3.4 3.5 + - - -
270A ILE* 3.6 22.9 - - + +
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Residues in contact with CYS 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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109A PRO* 3.5 30.8 - - + +
110A ARG* 4.0 5.8 - - - -
112A TRP* 4.2 1.0 - - - -
113A TRP* 3.7 28.0 - - + -
250A GLY 3.8 20.2 - - - -
251A VAL 3.5 9.0 - - - +
252A THR 3.0 0.4 - - - -
253A ALA* 1.3 78.8 - - - +
255A HIS* 1.3 60.6 + - - +
257A ALA* 3.4 4.5 + - - +
258A LEU* 3.2 23.4 + - - +
270A ILE* 3.6 27.8 - - - -
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Residues in contact with HIS 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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105A SER* 3.0 28.5 + - - -
106A PHE* 3.1 22.7 - - - -
109A PRO* 3.1 32.5 - - + +
212A PHE* 4.0 19.2 - + + -
215A PHE* 4.0 21.7 - + + -
216A LEU* 4.7 14.6 - - + -
222A GLU* 5.2 6.5 - - - +
252A THR* 3.1 29.8 + - + +
253A ALA 2.9 1.6 - - - -
254A CYS* 1.3 81.0 - - - +
256A ILE* 1.3 61.5 + - - +
258A LEU* 4.2 5.8 - - + +
259A ALA* 3.2 22.2 + - - +
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Residues in contact with ILE 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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179A VAL* 3.9 24.2 - - + +
181A SER* 4.0 17.7 - - - +
210A MET* 3.9 18.4 - - + +
215A PHE* 3.4 31.0 - - + -
232A PHE* 4.0 15.4 - - + -
243A LEU* 4.1 26.7 - - + -
245A ALA* 3.9 13.7 - - + -
253A ALA 2.7 13.7 + - - +
255A HIS* 1.3 77.8 - - - +
257A ALA* 1.3 57.0 + - - +
259A ALA* 3.1 3.8 + - - +
260A ALA* 2.9 26.9 + - - +
268A VAL* 4.7 0.9 - - + -
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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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112A TRP* 3.8 14.8 - - + -
113A TRP* 5.1 4.0 - - + -
116A ARG* 4.9 5.0 + - - +
253A ALA 3.4 3.1 + - - +
254A CYS* 3.8 14.6 - - - +
255A HIS 3.3 0.2 - - - -
256A ILE* 1.3 80.8 - - - +
258A LEU* 1.3 60.3 + - - +
260A ALA* 3.3 2.1 + - - +
261A TYR* 3.0 23.6 + - - +
265A LYS 4.4 1.9 - - - +
268A VAL* 3.9 35.7 - - + +
270A ILE* 4.5 8.7 - - + -
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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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8A ALA* 4.4 13.5 - - + +
9A LEU* 4.7 9.0 - - + -
109A PRO* 5.0 13.2 - - + -
112A TRP* 3.3 50.0 - - + +
125A VAL* 4.2 22.7 - - + -
222A GLU* 3.4 32.8 - - - +
254A CYS 3.2 13.8 + - - +
255A HIS* 4.2 7.4 - - + +
257A ALA* 1.3 73.3 - - - +
259A ALA* 1.3 69.9 + - - +
261A TYR* 3.7 1.2 - - - +
262A LEU* 3.1 30.7 + - + +
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Residues in contact with ALA 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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215A PHE* 3.9 26.9 - - + -
222A GLU* 3.9 18.8 - - - +
228A LEU* 4.0 11.4 - - + +
232A PHE* 4.1 8.5 - - + -
255A HIS 3.2 14.9 + - - +
256A ILE 3.1 5.3 + - - +
258A LEU* 1.3 86.2 - - - +
260A ALA* 1.3 60.9 + - - +
262A LEU* 3.4 3.6 + - - +
263A CYS* 3.3 22.5 + - - +
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Residues in contact with ALA 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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232A PHE* 4.0 9.7 - - + -
239A LEU* 4.0 14.4 - - + -
243A LEU* 5.3 0.9 - - + -
256A ILE* 2.9 12.8 + - + +
257A ALA 3.9 0.2 - - - +
258A LEU 3.2 0.2 - - - -
259A ALA* 1.3 77.2 - - - +
261A TYR* 1.3 52.9 + - - +
263A CYS* 2.7 28.6 + - - +
264A GLY 3.0 0.9 + - - -
265A LYS* 2.9 29.3 + - + +
268A VAL* 3.5 32.3 - - + -
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Residues in contact with TYR 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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3A GLN 5.0 1.2 + - - -
4A VAL 4.4 2.0 + - - -
5A LEU* 3.3 35.2 - - + +
6A TYR* 3.1 45.9 + - - +
8A ALA* 3.7 25.8 - - + -
112A TRP* 4.0 13.7 - + + -
116A ARG* 4.0 28.5 + - - -
121A ARG* 5.2 2.4 + - - +
257A ALA 3.0 17.6 + - - +
258A LEU* 3.7 5.4 - - - +
260A ALA* 1.3 69.0 - - - +
262A LEU* 1.3 63.9 + - + +
263A CYS 2.9 4.5 - - - -
264A GLY 2.9 10.2 + - - -
265A LYS 3.1 14.1 + - - +
266A PRO* 3.6 32.3 - - + -
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Residues in contact with LEU 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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8A ALA* 3.7 28.9 - - + +
9A LEU* 3.8 36.1 - - + +
222A GLU* 4.0 24.0 - - + +
223A LYS 5.5 0.4 - - - +
225A PRO* 3.9 25.4 - - + +
228A LEU* 4.4 11.4 - - + -
229A ARG* 5.3 0.2 + - - -
258A LEU* 3.1 23.9 + - + +
259A ALA 4.0 2.9 - - - +
261A TYR* 1.3 81.9 - - + +
263A CYS* 1.3 58.6 + - - +
264A GLY 3.3 1.3 - - - -
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Residues in contact with CYS 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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225A PRO* 3.8 17.0 - - - -
228A LEU* 3.7 26.9 - - - -
229A ARG* 3.2 40.5 + - - +
232A PHE* 4.7 2.9 - - - -
239A LEU* 4.1 20.2 - - + +
259A ALA 3.3 13.9 + - - +
260A ALA* 2.7 17.3 + - - +
262A LEU* 1.3 80.8 - - - +
264A GLY* 1.3 55.0 + - - +
265A LYS 3.5 0.8 + - - -
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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