Contacts of the helix formed by residues 666 - 679 (chain B) in PDB entry 1OFD
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 666 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545B LEU* 3.8 18.4 - - + -
546B VAL 3.7 8.7 - - - +
644B THR 3.6 9.9 - - - +
647B CYS* 3.6 21.8 - - + +
653B PHE* 3.6 30.7 - - + -
664B ILE* 3.4 16.6 - - + +
665B CYS* 1.3 80.3 - - - +
667B TYR* 1.3 63.9 + - - +
668B LEU 3.3 2.7 - - - -
669B ALA* 3.2 6.1 + - + -
670B LEU* 3.1 31.2 + - + +
703B TYR* 4.5 2.7 - - + -
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Residues in contact with TYR 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B LEU* 3.7 18.1 - - + +
437B PHE* 5.0 10.1 - + - -
446B GLN* 5.5 1.4 + - - -
450B PHE* 4.3 4.9 - - - -
548B GLU* 3.5 12.1 - - - +
602B ASP* 2.7 26.6 + - - -
603B ARG* 3.4 68.2 - - + +
608B ILE* 6.5 0.7 - - + -
643B ASP* 3.5 11.2 - - - -
644B THR* 3.3 14.1 + - - -
645B ALA* 3.3 32.1 - - + +
665B CYS* 2.9 14.4 + - - -
666B PRO* 1.3 72.5 - - - +
668B LEU* 1.3 74.3 + - + +
670B LEU* 3.5 6.5 + - - +
671B GLU* 3.1 26.3 + - - +
674B ARG* 4.6 0.5 + - - -
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Residues in contact with LEU 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B PHE* 4.2 17.9 - - + -
443B VAL* 4.9 6.3 - - + +
446B GLN* 3.9 16.4 - - + +
447B GLN* 3.8 32.1 - - + +
452B TYR* 3.4 33.9 - - + +
644B THR 4.2 2.0 + - - -
645B ALA* 3.6 26.9 - - + -
666B PRO 3.3 0.6 - - - -
667B TYR* 1.3 85.4 - - + +
669B ALA* 1.3 60.5 + - - +
671B GLU* 4.0 15.5 - - + -
672B SER* 2.8 37.9 + - - +
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Residues in contact with ALA 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B TYR* 3.1 12.0 + - - -
461B VAL* 4.5 2.8 - - + +
645B ALA 4.8 0.2 + - - -
647B CYS 3.3 19.9 + - - +
648B TRP* 3.9 8.5 - - + -
666B PRO* 3.2 10.4 + - + +
668B LEU* 1.3 75.7 - - - +
670B LEU* 1.3 63.1 + - - +
672B SER* 3.2 9.0 + - - -
673B VAL* 3.1 26.2 + - - +
703B TYR* 3.3 31.2 - - + +
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Residues in contact with LEU 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B PHE* 4.5 13.9 - - + -
545B LEU* 4.6 4.9 - - + -
546B VAL 4.7 0.2 - - - +
547B ASN* 3.9 33.4 - - + -
548B GLU* 4.4 7.0 - - + +
665B CYS* 5.0 1.1 - - - -
666B PRO* 3.1 33.6 + - + +
667B TYR* 3.8 8.1 - - - +
669B ALA* 1.3 74.8 - - - +
671B GLU* 1.3 56.9 + - - +
673B VAL* 3.3 6.2 + - - +
674B ARG* 3.0 51.5 + - - +
700B LEU* 3.6 18.0 - - + +
703B TYR* 3.9 28.9 - - + -
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Residues in contact with GLU 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B THR* 3.2 7.2 - - - -
436B LEU* 2.8 37.4 + - + +
437B PHE* 3.3 27.6 + - + -
443B VAL* 4.9 1.8 - - + -
667B TYR 3.1 17.7 + - - +
668B LEU* 3.7 13.5 - - + +
670B LEU* 1.3 74.9 - - - +
672B SER* 1.3 58.2 + - - +
674B ARG* 2.6 36.5 + - - +
675B GLN* 2.8 66.0 + - + +
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Residues in contact with SER 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B VAL* 5.4 0.7 - - - -
447B GLN* 2.8 33.4 + - - +
452B TYR* 3.8 14.9 - - - -
457B VAL* 5.6 4.5 - - - -
461B VAL* 4.3 15.5 - - - -
668B LEU* 2.8 24.8 + - - +
669B ALA* 3.2 11.9 + - - -
671B GLU* 1.3 72.7 - - - +
673B VAL* 1.3 57.6 + - - +
675B GLN* 3.4 4.8 + - - +
676B TRP* 2.9 31.4 + - - +
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Residues in contact with VAL 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B VAL* 3.8 20.0 - - + -
465B ALA* 3.8 28.7 - - + -
669B ALA 3.1 14.8 + - - +
670B LEU* 3.5 8.7 - - - +
671B GLU 3.2 0.2 - - - -
672B SER* 1.3 74.4 - - - +
674B ARG* 1.3 65.7 + - - +
676B TRP* 3.6 7.9 - - + +
677B TRP* 2.9 23.9 + - - +
696B LEU* 5.0 0.7 - - + -
699B ALA* 4.0 21.1 - - + -
700B LEU* 3.8 19.3 - - + -
703B TYR* 4.1 18.8 - - + -
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Residues in contact with ARG 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B PHE* 5.9 1.6 - - - +
432B ALA* 2.9 29.4 + - - +
433B GLU* 3.5 21.3 - - - +
434B LYS 3.5 15.7 + - - -
435B THR* 4.1 10.5 - - + +
436B LEU* 4.0 11.7 - - - +
548B GLU* 3.8 26.9 + - - +
667B TYR 4.6 0.4 + - - -
670B LEU* 3.0 32.1 + - - +
671B GLU* 2.6 57.9 + - - +
673B VAL* 1.3 77.5 - - - +
675B GLN* 1.3 57.3 + - - +
677B TRP* 3.3 2.1 + - - +
678B LEU* 2.9 37.3 + - + +
696B LEU* 4.0 17.0 - - + -
700B LEU* 4.3 12.6 - - + +
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Residues in contact with GLN 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B THR* 3.5 15.0 - - - +
437B PHE 3.3 18.6 + - - -
438B ASN 5.7 0.4 - - - -
439B ASP 5.4 1.0 + - - -
440B ALA* 5.1 7.6 - - - +
443B VAL* 3.6 39.6 - - + +
447B GLN* 6.0 0.2 - - - +
671B GLU* 2.8 46.5 + - + +
672B SER* 4.0 3.4 - - - +
674B ARG* 1.3 70.5 - - - +
676B TRP* 1.3 61.9 + - - +
678B LEU* 3.4 7.2 + - - +
679B ASP* 2.9 29.8 + - - +
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Residues in contact with TRP 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B VAL* 6.0 3.1 - - + -
461B VAL* 6.4 0.7 - - + -
462B VAL* 3.4 41.2 - - + +
465B ALA* 4.2 16.6 - - + -
466B SER* 3.7 27.6 - - - -
672B SER 2.9 18.6 + - - +
673B VAL* 3.6 10.8 - - + +
675B GLN* 1.3 75.6 - - - +
677B TRP* 1.3 83.7 + + + +
679B ASP* 3.2 11.8 - - + +
682B THR* 2.7 55.1 + - + -
686B MET* 5.5 4.7 - - - -
690B ARG* 2.9 33.6 - - + +
694B ILE* 5.2 6.7 - - + -
699B ALA* 4.1 23.1 - - + -
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Residues in contact with TRP 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673B VAL 2.9 18.4 + - - +
674B ARG 3.6 3.4 - - - +
676B TRP* 1.3 92.1 - + + +
678B LEU* 1.3 81.1 + - + +
679B ASP 3.5 3.5 + - - +
682B THR* 4.0 8.5 - - + +
683B GLN* 2.8 47.7 + - - +
686B MET* 3.6 15.9 - - + +
694B ILE* 3.1 27.5 + - + -
695B ASP* 3.4 20.1 - - + -
696B LEU* 3.4 46.2 - - + -
699B ALA* 4.4 9.9 - - + -
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Residues in contact with LEU 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B GLU 5.3 0.7 - - - +
435B THR* 3.4 33.0 - - + -
674B ARG* 2.9 26.0 + - + +
675B GLN* 4.1 9.4 - - - +
677B TRP* 1.3 100.3 - - + +
679B ASP* 1.3 65.0 + - - +
680B GLU* 3.3 4.0 + - - -
683B GLN* 3.9 10.1 + - - +
696B LEU* 5.0 7.6 - - + -
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Residues in contact with ASP 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675B GLN 2.9 13.4 + - - +
676B TRP* 3.2 18.3 + - + +
677B TRP 3.8 1.0 - - - +
678B LEU* 1.3 77.6 - - - +
680B GLU* 1.3 80.3 + - - +
681B LYS* 3.2 42.0 + - - +
682B THR* 3.0 18.7 + - - +
683B GLN* 3.3 10.4 + - - +
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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