Contacts of the strand formed by residues 349 - 362 (chain A) in PDB entry 2OR4
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 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A SER* 3.4 1.9 - - - -
119A TYR 3.0 31.8 + - - +
120A PRO 5.4 0.9 + - - -
121A ASN* 5.4 2.7 + - + +
167A GLN* 3.3 25.8 - - - +
347A HIS 3.7 5.4 - - - +
348A SER* 1.3 74.7 - - - +
350A ASN* 1.3 69.9 + - - +
351A GLU* 2.8 23.0 + - - +
1757A NAG 3.7 33.3 + - + +
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Residues in contact with ASN 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.9 17.9 - - + +
117A LEU 3.1 7.2 - - - +
118A SER* 3.4 23.0 + - - -
164A PHE* 3.6 22.9 + - - -
165A SER 4.7 5.4 + - - +
166A PRO* 5.9 2.0 - - - +
283A ILE* 4.0 21.1 - - + +
289A LEU* 4.2 15.4 - - - +
349A THR* 1.3 77.6 - - - +
351A GLU* 1.3 61.2 + - - +
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Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.9 4.6 - - - +
117A LEU 2.8 32.5 + - - +
119A TYR* 3.5 35.3 - - + +
349A THR* 2.8 29.9 + - - +
350A ASN* 1.3 76.7 - - - +
352A VAL* 1.3 63.0 + - - +
353A THR* 2.9 19.4 + - - +
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASP* 3.7 36.3 - - + +
115A VAL 3.3 4.5 - - - -
116A LEU* 4.1 9.6 - - + +
268A LEU* 3.6 30.5 - - + -
280A ARG* 4.6 13.5 - - - +
351A GLU* 1.3 73.5 - - - +
353A THR* 1.3 63.7 + - - +
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Residues in contact with THR 353 (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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85A GLY* 3.6 38.4 - - - +
113A TYR 3.7 0.2 - - - +
114A ASP* 4.2 3.6 - - - -
115A VAL* 2.8 32.4 + - - +
117A LEU* 3.7 12.7 - - - +
119A TYR* 3.9 12.4 - - + +
351A GLU* 2.9 27.9 + - - +
352A VAL* 1.3 75.9 + - - +
354A ARG* 1.3 66.6 + - - +
355A ILE* 3.6 0.9 + - - +
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Residues in contact with ARG 354 (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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85A GLY* 3.7 17.8 - - - -
112A HIS* 3.5 36.3 + - + -
113A TYR 3.3 8.5 - - - +
114A ASP* 2.9 38.4 + - - +
276A GLU* 5.7 3.8 - - - +
353A THR* 1.3 78.7 - - - +
355A ILE* 1.3 69.6 + - - +
356A TYR* 3.2 42.7 + - + +
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Residues in contact with ILE 355 (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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85A GLY 4.6 2.9 - - - +
111A ALA 4.7 0.2 - - - -
112A HIS* 3.1 27.2 - - - +
113A TYR* 2.8 34.0 + - + +
115A VAL* 3.7 39.3 - - + -
117A LEU* 4.2 12.8 - - + -
353A THR 4.1 1.6 - - - +
354A ARG* 1.3 79.2 - - - +
356A TYR* 1.3 65.9 + - - +
357A ASN* 5.2 0.4 - - - +
422A ASP* 3.3 17.0 - - + +
423A ALA* 4.0 20.2 - - + -
429A LEU 4.2 1.1 - - - +
430A GLY* 3.7 34.5 - - - +
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Residues in contact with TYR 356 (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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90A PHE* 3.6 61.4 - + + -
93A ALA* 4.3 11.7 - - + -
110A LEU* 4.1 18.8 - - + -
111A ALA 3.7 2.5 - - - -
112A HIS* 3.7 25.1 - + + -
354A ARG* 3.2 40.8 - - + +
355A ILE* 1.3 77.3 - - - +
357A ASN* 1.3 60.8 + - - +
378A ARG* 2.7 38.0 + - - +
422A ASP* 2.8 20.3 + - - +
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Residues in contact with ASN 357 (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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110A LEU* 3.3 5.6 - - - -
111A ALA* 2.8 39.7 + - + +
113A TYR* 3.6 15.2 - - - -
355A ILE* 4.4 0.6 - - - -
356A TYR* 1.3 74.3 - - - +
358A VAL* 1.3 62.3 + - - +
359A ILE* 4.2 10.8 - - + -
420A SER 3.3 7.0 - - - +
421A TRP* 3.5 16.1 - - + -
422A ASP* 2.9 25.5 + - - +
430A GLY* 2.9 34.5 + - - -
434A TRP* 3.5 18.8 - - - +
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Residues in contact with VAL 358 (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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93A ALA* 3.6 25.1 - - + +
96A ILE* 4.4 4.7 - - + -
97A GLN* 3.9 17.3 - - + +
100A TRP* 3.9 12.9 - - + -
108A VAL* 3.5 27.4 - - + -
109A GLU 3.6 4.7 - - - +
110A LEU* 3.7 10.3 - - + -
357A ASN* 1.3 72.8 - - - +
359A ILE* 1.3 65.1 + - - +
360A GLY 4.1 0.2 - - - -
378A ARG* 4.0 10.3 - - - +
418A PHE 3.6 0.5 - - - +
419A ALA* 3.3 5.0 - - - -
420A SER* 3.0 49.7 + - - -
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Residues in contact with ILE 359 (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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107A SER* 4.0 0.9 + - - +
108A VAL* 3.4 3.1 - - - -
109A GLU* 2.8 44.5 + - + +
111A ALA* 4.4 9.0 - - + -
357A ASN* 4.2 10.5 - - + +
358A VAL* 1.3 81.1 - - - +
360A GLY* 1.3 63.6 - - - +
361A THR* 4.9 8.0 + - - +
417A LEU* 5.2 9.9 - - + -
418A PHE 3.5 4.0 - - - +
419A ALA* 3.9 8.7 - - + -
421A TRP* 3.7 26.9 - - + -
434A TRP* 3.6 45.8 - - + +
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Residues in contact with GLY 360 (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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100A TRP* 4.0 8.4 - - - -
105A LEU* 3.7 21.8 - - - -
107A SER 3.3 9.0 - - - -
108A VAL* 4.2 3.1 - - - -
359A ILE* 1.3 74.8 - - - +
361A THR* 1.3 62.2 + - - -
416A ILE 3.9 0.5 - - - +
417A LEU* 3.3 7.5 - - - +
418A PHE* 2.9 35.1 + - - -
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Residues in contact with THR 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.7 5.9 - - - +
106A ASP* 3.0 29.8 + - + +
107A SER* 2.9 28.9 + - - +
359A ILE* 4.9 6.2 + - - +
360A GLY* 1.3 75.3 - - - -
362A LEU* 1.3 63.4 + - - +
363A ARG* 4.0 15.3 - - + +
415A THR* 4.1 9.6 - - + -
416A ILE 3.6 2.9 - - - -
417A LEU* 3.5 22.3 - - + +
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Residues in contact with LEU 362 (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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104A GLY 4.9 0.7 - - - +
105A LEU* 4.1 17.2 - - + +
106A ASP* 3.4 9.6 - - - +
361A THR* 1.3 75.2 - - - +
363A ARG* 1.3 65.0 + - - +
402A PHE* 4.0 32.3 - - + +
403A GLY* 5.4 0.4 - - - +
406A LYS* 3.6 37.0 - - + -
410A TRP* 4.4 6.7 - - + -
411A ARG* 4.0 5.4 - - - +
412A PRO* 3.8 29.4 - - + +
415A THR* 3.4 0.9 - - - -
416A ILE* 2.9 40.5 + - + +
418A PHE* 4.2 7.4 - - + -
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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