Contacts of the helix formed by residues 505 - 518 (chain A) in PDB entry 3O8C
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 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503A GLU 4.0 1.5 + - - +
504A LEU* 1.3 76.0 - - - +
506A PRO* 1.3 73.7 - - - +
507A ALA* 3.6 10.1 + - - +
508A GLU* 2.9 51.2 + - - +
509A THR* 3.0 10.5 + - - -
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Residues in contact with PRO 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TYR* 3.4 20.0 - - + -
499A CYS* 4.3 12.3 - - - -
504A LEU 4.1 3.4 - - - +
505A THR* 1.3 85.2 - - - +
507A ALA* 1.3 56.7 + - - +
509A THR* 3.3 2.3 + - - +
510A SER* 2.9 31.4 + - - -
533A GLU* 3.7 16.6 - - + +
536A PHE* 3.7 26.5 - - + +
537A THR* 3.7 28.9 - - + +
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Residues in contact with ALA 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A THR* 3.2 9.3 - - - +
506A PRO* 1.3 79.4 - - - +
508A GLU* 1.3 62.5 + - + +
510A SER* 3.2 4.9 + - - -
511A VAL* 3.2 25.2 + - - +
533A GLU* 3.6 22.0 + - - +
537A THR* 5.3 0.2 + - - -
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Residues in contact with GLU 508 (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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503A GLU 3.9 5.2 - - - +
504A LEU* 3.5 21.6 - - + +
505A THR* 2.9 49.4 + - - +
507A ALA* 1.3 73.7 - - + +
509A THR* 1.3 66.7 + - - +
511A VAL* 3.2 17.8 + - - +
512A ARG* 3.3 21.3 + - - +
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Residues in contact with THR 509 (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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301A LEU* 4.2 9.2 - - + -
494A CYS 4.0 13.9 + - - +
495A TYR* 3.7 23.1 - - + -
498A GLY* 4.0 9.0 - - - -
499A CYS* 6.2 0.2 - - - -
504A LEU* 3.4 25.8 + - - +
505A THR 3.0 8.3 + - - -
506A PRO* 3.6 8.2 - - - +
508A GLU* 1.3 77.8 - - - +
510A SER* 1.3 61.5 + - - +
512A ARG* 3.1 11.0 + - - +
513A LEU* 3.0 45.1 + - + +
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Residues in contact with SER 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TYR* 2.7 27.3 + - - -
506A PRO 2.9 11.8 + - - -
507A ALA 3.5 7.4 - - - -
508A GLU 3.2 0.2 - - - -
509A THR* 1.3 77.6 - - - +
511A VAL* 1.3 56.3 - - - +
513A LEU* 3.8 2.0 - - - -
514A ARG* 2.9 32.4 + - - +
529A LEU* 3.8 10.1 + - - +
533A GLU* 2.6 33.4 + - - +
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Residues in contact with VAL 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ASP* 3.4 32.0 - - - +
507A ALA 3.2 13.2 + - - +
508A GLU* 3.2 11.4 + - - +
510A SER* 1.3 78.3 - - - +
512A ARG* 1.3 64.3 + - + +
514A ARG* 3.4 5.3 + - - +
515A ALA* 3.2 20.3 + - - +
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Residues in contact with ARG 512 (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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274A LEU* 3.7 16.0 + - - +
277A GLY* 4.3 13.7 + - - -
301A LEU* 4.0 18.6 - - + -
304A GLY* 3.2 30.4 - - - +
305A THR* 2.9 38.6 + - + +
308A ASP* 4.6 7.6 - - + +
309A GLN* 3.4 25.8 - - - +
502A TYR* 6.0 0.4 - - - +
504A LEU* 3.7 37.0 - - - +
508A GLU* 3.3 16.4 + - - +
509A THR 3.1 5.1 + - - +
511A VAL* 1.3 81.3 - - + +
513A LEU* 1.3 64.0 + - - +
515A ALA 3.2 1.9 + - - -
516A TYR 3.1 16.5 + - - -
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Residues in contact with LEU 513 (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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300A ILE* 3.8 29.8 - - + +
301A LEU* 4.3 15.0 - - + -
491A LEU* 4.4 10.3 - - + -
494A CYS* 3.8 22.7 - - + -
495A TYR* 3.5 32.8 - - + -
509A THR* 3.0 29.0 + - + +
510A SER 4.0 0.4 - - - +
512A ARG* 1.3 76.5 - - - +
514A ARG* 1.3 58.0 + - - +
516A TYR* 3.2 5.8 + - - +
517A LEU* 2.9 32.2 + - + +
529A LEU* 3.6 24.7 - - + -
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Residues in contact with ARG 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A SER 2.9 19.5 + - - +
511A VAL* 3.8 6.1 - - - +
512A ARG 3.2 0.4 - - - -
513A LEU* 1.3 73.0 - - - +
515A ALA* 1.3 61.8 + - - +
517A LEU* 3.3 13.3 + - - +
518A ASN* 2.9 67.2 + - - +
527A ASP* 2.7 41.6 + - - +
529A LEU* 3.6 25.3 - - + +
530A GLU* 5.3 10.3 + - - +
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Residues in contact with ALA 515 (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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304A GLY 3.8 14.1 - - - +
307A LEU* 4.1 7.2 - - + -
308A ASP* 3.8 22.7 - - + +
511A VAL 3.2 12.7 + - - +
512A ARG 3.2 8.9 + - - +
514A ARG* 1.3 80.2 - - - +
516A TYR* 1.3 57.4 + - - +
518A ASN* 3.5 5.9 + - - +
519A THR* 2.8 28.4 + - - -
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Residues in contact with TYR 516 (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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292A CYS 4.5 2.3 + - - -
294A SER 4.5 2.0 + - - -
299A THR* 6.0 0.2 - - + -
300A ILE* 3.5 52.3 - - + +
303A ILE* 3.8 32.5 - - + -
304A GLY* 3.8 12.6 - - - -
307A LEU* 4.0 8.5 - - - -
486A PHE* 4.0 13.6 - + - -
512A ARG 3.1 7.1 + - - +
513A LEU* 3.4 10.5 - - - +
514A ARG 3.2 0.2 - - - -
515A ALA* 1.3 76.6 - - - +
517A LEU* 1.3 74.7 + - + +
519A THR* 3.1 21.5 + - - +
522A LEU* 4.0 16.6 - - + +
523A PRO* 3.2 50.4 - - - +
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Residues in contact with LEU 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A PHE* 4.6 5.4 - - + -
491A LEU* 5.1 7.4 - - + -
513A LEU 2.9 21.2 + - - +
514A ARG* 4.0 11.2 - - - +
516A TYR* 1.3 89.3 - - + +
518A ASN* 1.3 61.4 + - - +
519A THR 3.2 3.4 + - - +
523A PRO 5.4 1.6 - - - +
524A VAL* 5.5 0.9 - - - -
525A CYS* 4.4 31.4 - - + +
526A GLN 4.8 3.1 - - - +
527A ASP* 4.0 40.2 - - + +
529A LEU* 4.0 21.1 - - + -
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Residues in contact with ASN 518 (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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514A ARG* 2.9 51.6 + - - +
515A ALA* 4.0 6.2 - - - +
516A TYR 3.2 0.4 - - - -
517A LEU* 1.3 78.9 - - - +
519A THR* 1.3 61.2 + - - +
520A PRO* 3.7 7.6 - - - +
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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