Contacts of the helix formed by residues 388 - 408 (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 PRO 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A HIS* 3.2 36.1 - - + +
378A ARG* 3.7 11.0 - - - +
379A ASP 3.4 27.1 - - - +
380A SER* 3.7 12.8 - - - -
384A GLY* 4.3 0.7 - - - -
386A ILE 3.2 4.5 - - - +
387A ASP* 1.3 82.0 - - - +
389A GLN* 1.4 68.5 + - - +
390A SER 3.2 2.7 - - - -
391A GLY* 2.8 21.3 + - - -
392A ALA 3.0 9.2 + - - -
453A ASP* 3.2 22.8 - - - +
454A SER* 4.4 0.2 - - - +
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Residues in contact with GLN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 3.4 6.9 - - + +
77A PHE* 3.6 41.6 + - + +
78A THR* 3.6 16.8 - - + -
82A HIS* 4.1 11.1 + - - -
92A LEU* 4.2 6.5 - - - +
378A ARG* 2.8 31.1 + - - +
380A SER* 4.5 4.9 - - - -
383A PHE 4.1 1.8 + - - +
384A GLY 3.0 25.4 + - - +
388A PRO* 1.4 85.0 - - + +
390A SER* 1.3 56.9 + - - +
392A ALA* 3.3 20.4 - - - +
393A ALA* 2.9 32.7 + - - +
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 3.5 8.4 - - - +
385A GLY 3.8 9.5 + - - -
386A ILE* 2.7 30.2 + - - +
389A GLN* 1.3 78.0 - - - +
391A GLY* 1.3 59.1 + - - +
393A ALA* 4.3 0.8 - - - +
394A VAL* 3.5 13.7 + - - +
454A SER* 3.3 2.8 - - - -
455A SER* 2.8 34.3 + - - -
456A ILE* 3.9 7.4 + - - -
573A HIS* 3.2 31.5 - - - -
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Residues in contact with GLY 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PRO 2.8 7.6 + - - -
390A SER* 1.3 80.2 + - - +
392A ALA* 1.3 57.6 + - - -
393A ALA 3.2 1.6 - - - -
394A VAL* 3.0 5.4 + - - +
395A VAL* 2.9 29.3 + - - +
452A ALA 3.7 9.9 - - - -
453A ASP 3.2 25.1 + - - -
454A SER* 4.0 0.4 - - - +
455A SER* 3.4 8.4 - - - +
580A ARG* 3.7 2.3 + - - -
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.8 11.3 - - + -
96A ILE* 6.3 0.4 - - + -
376A GLY 6.1 0.9 - - - +
377A HIS 4.1 15.7 + - - +
378A ARG* 5.1 3.8 - - + -
388A PRO 3.0 10.2 + - - +
389A GLN* 3.3 26.5 - - - +
391A GLY* 1.3 73.7 - - - +
393A ALA* 1.3 57.5 + - - +
395A VAL* 3.3 9.3 + - - +
396A HIS* 2.9 29.5 + - - +
420A SER* 6.0 0.9 - - - +
452A ALA 4.1 2.5 + - - -
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Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.7 33.4 - - + +
73A PHE* 3.8 9.0 - - + -
74A LEU* 3.7 18.8 - - + +
77A PHE* 3.8 10.9 - - + -
389A GLN 2.9 18.6 + - - +
390A SER* 4.3 2.9 - - - +
392A ALA* 1.3 75.8 - - - +
394A VAL* 1.3 58.4 + - - +
396A HIS* 3.4 3.3 + - - +
397A GLU* 3.1 28.2 + - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 4.1 22.9 - - + -
390A SER 3.5 5.1 + - - +
391A GLY 3.0 10.3 + - - +
393A ALA* 1.3 76.6 - - - +
395A VAL* 1.3 66.3 + - + +
397A GLU* 3.2 3.5 + - - +
398A ILE* 2.9 33.5 + - + +
455A SER* 3.2 26.2 - - - +
573A HIS* 3.7 21.8 - - + +
576A VAL 4.5 0.2 - - - -
577A ALA* 3.6 27.5 - - + +
580A ARG* 4.2 14.1 - - - -
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Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TRP* 3.9 26.9 - - + -
374A LEU* 4.3 23.3 - - + +
375A GLY 5.2 0.2 - - - -
376A GLY* 5.1 6.5 - - - +
391A GLY 2.9 13.8 + - - +
392A ALA* 3.3 9.4 + - - +
394A VAL* 1.3 75.6 - - + +
396A HIS* 1.3 58.0 + - - +
398A ILE* 3.1 9.4 + - + +
399A VAL* 2.8 35.0 + - + +
418A PHE* 4.8 2.7 - - + -
419A ALA 4.9 7.4 - - - +
452A ALA* 3.3 37.0 - - + +
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Residues in contact with HIS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 3.7 34.3 - + + -
77A PHE* 3.7 17.6 - + + -
96A ILE* 3.5 25.8 - - + +
99A GLN* 2.9 32.8 + - + -
100A TRP* 2.9 42.7 + + - +
103A PHE* 3.6 23.0 - + - -
392A ALA 2.9 17.7 + - - +
393A ALA 3.5 7.2 - - - +
394A VAL 3.3 0.2 - - - -
395A VAL* 1.3 76.2 - - - +
397A GLU* 1.3 58.1 + - - +
399A VAL* 3.3 1.4 + - - +
400A ARG* 2.9 22.9 + - - +
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Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 3.6 16.2 - - + -
66A LYS 2.8 22.7 + - - +
69A ASN* 3.0 21.8 + - - +
70A ILE* 3.9 24.5 - - + -
73A PHE* 3.5 9.5 - - + -
393A ALA 3.1 16.7 + - - +
394A VAL 3.2 3.8 + - - +
396A HIS* 1.3 73.5 - - - +
398A ILE* 1.3 60.4 + - - +
400A ARG* 2.7 48.4 + - - +
401A SER* 3.0 27.4 + - - -
577A ALA* 5.7 0.7 - - + -
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Residues in contact with ILE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 4.0 4.3 - - + -
65A LEU* 3.9 15.9 - - + -
374A LEU* 3.7 28.9 - - + -
394A VAL* 2.9 35.8 + - + +
395A VAL* 3.1 7.6 + - + +
397A GLU* 1.3 73.6 - - - +
399A VAL* 1.3 67.6 + - - +
401A SER* 3.3 1.9 + - - -
402A PHE* 2.9 51.4 + - + -
418A PHE* 4.2 1.6 - - + -
577A ALA* 3.7 14.8 - - + +
580A ARG* 4.1 5.8 - - + -
581A GLY* 3.6 26.7 - - - +
584A VAL* 5.7 0.2 - - + -
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TRP* 3.9 26.7 - - + +
103A PHE* 3.9 18.6 - - + +
105A LEU* 3.9 33.8 - - + +
395A VAL* 2.8 24.5 + - + +
396A HIS 3.6 6.7 - - - +
398A ILE* 1.3 72.3 - - - +
400A ARG* 1.3 58.9 + - - +
402A PHE* 3.3 1.6 + - - +
403A GLY* 2.9 28.2 + - - -
418A PHE* 3.5 39.3 - - + -
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Residues in contact with ARG 400 (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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64A GLU* 3.0 47.1 + - - +
65A LEU* 4.7 0.2 - - - +
66A LYS* 4.4 1.2 - - - +
69A ASN* 3.3 17.5 - - - +
73A PHE* 4.5 8.5 - - - -
103A PHE* 3.8 40.7 - - + +
396A HIS 2.9 15.3 + - - +
397A GLU* 2.7 47.3 + - - +
398A ILE 3.2 0.4 - - - -
399A VAL* 1.3 77.7 - - - +
401A SER* 1.3 56.9 + - - +
403A GLY* 3.4 1.4 + - - -
404A THR* 2.9 43.4 + - - +
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Residues in contact with SER 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 2.8 44.1 + - - -
64A GLU* 3.3 27.7 - - - +
65A LEU* 3.7 12.6 - - - -
397A GLU 3.0 16.8 + - - -
398A ILE 3.8 0.2 - - - -
400A ARG* 1.3 74.5 - - - +
402A PHE* 1.4 64.5 + - - +
404A THR* 3.1 12.3 + - - -
405A LEU* 3.2 15.2 + - - +
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Residues in contact with PHE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 3.5 27.1 - + - -
105A LEU* 5.6 0.4 - - + -
362A LEU* 4.0 14.1 - - + +
398A ILE* 2.9 41.3 + - + +
399A VAL 3.9 3.1 - - - +
401A SER* 1.4 75.5 - - - +
403A GLY* 1.3 57.7 + - - +
405A LEU* 3.3 7.9 + - + +
406A LYS* 3.0 27.6 + - - +
410A TRP* 3.5 29.1 - + - -
416A ILE* 3.8 20.2 - - + -
418A PHE* 3.7 19.1 - + + -
581A GLY 4.1 0.9 - - - -
584A VAL* 3.9 22.2 - - + -
585A PHE* 3.7 35.4 - + - -
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Residues in contact with GLY 403 (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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103A PHE 3.1 26.6 - - - +
104A GLY* 4.5 6.2 - - - -
105A LEU* 5.4 4.9 - - - +
362A LEU* 5.4 0.6 - - - +
399A VAL 2.9 15.8 + - - -
400A ARG 3.7 0.7 - - - -
402A PHE* 1.3 75.8 - - - +
404A THR* 1.3 56.1 + - - +
406A LYS* 3.2 8.8 + - - +
407A LYS* 2.9 33.6 + - - +
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Residues in contact with THR 404 (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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64A GLU* 4.1 24.2 - - + +
400A ARG* 2.9 35.7 + - - +
401A SER 3.1 9.1 + - - -
403A GLY* 1.3 74.9 - - - +
405A LEU* 1.3 64.3 + - + +
407A LYS* 3.3 17.0 + - - +
408A GLU* 3.4 31.1 + - - +
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Residues in contact with LEU 405 (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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56A HIS* 3.3 30.0 - - + +
57A ASN 4.8 1.8 - - - +
60A ALA* 4.1 19.3 - - + +
61A PHE* 3.9 36.6 - - + +
64A GLU* 6.3 2.0 - - + -
401A SER 3.2 10.4 + - - +
402A PHE* 3.3 4.2 + - + +
404A THR* 1.3 75.0 - - + +
406A LYS* 1.3 68.0 + - - +
408A GLU* 3.1 20.5 + - - +
409A GLY 3.3 0.3 + - - -
410A TRP* 3.1 53.3 + - + +
585A PHE* 4.3 9.0 - - + -
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLY* 2.6 34.6 + - - +
105A LEU 4.5 1.0 + - - -
106A ASP* 3.5 27.6 + - - +
362A LEU* 3.6 23.8 - - + -
402A PHE 3.0 14.3 + - - +
403A GLY* 3.2 9.2 + - - +
405A LEU* 1.3 77.5 - - - +
407A LYS* 1.3 59.7 + - + +
409A GLY* 2.9 20.4 + - - -
410A TRP* 3.1 21.6 + - + +
411A ARG* 3.5 19.7 - - + +
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Residues in contact with LYS 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU 2.8 28.2 + - - -
103A PHE* 3.7 17.8 + - - +
104A GLY* 4.0 9.4 - - - -
403A GLY 2.9 19.2 + - - +
404A THR* 3.8 9.2 - - - +
405A LEU 3.2 0.4 - - - -
406A LYS* 1.3 77.8 - - + +
408A GLU* 1.3 59.1 + - + +
409A GLY 3.2 2.2 + - - -
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Residues in contact with GLU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 2.7 44.7 + - + +
404A THR* 3.4 32.0 - - - +
405A LEU* 3.1 11.7 + - - +
407A LYS* 1.3 77.5 - - + +
409A GLY* 1.3 56.7 + - - +
410A TRP 3.6 0.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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