Contacts of the helix formed by residues 666 - 678 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545A LEU* 3.7 16.8 - - + -
546A VAL 3.7 9.4 - - - +
644A THR 3.5 9.6 - - - +
647A CYS* 3.5 24.2 - - + +
653A PHE* 3.7 30.3 - - + -
664A ILE* 3.5 14.1 - - + +
665A CYS* 1.3 80.4 - - - +
667A TYR* 1.3 63.9 + - - +
668A LEU 3.4 2.5 - - - -
669A ALA* 3.1 6.0 + - + -
670A LEU* 3.1 30.6 + - + +
703A TYR* 4.5 5.8 - - + -
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Residues in contact with TYR 667 (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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436A LEU* 3.9 18.6 - - + +
437A PHE* 5.0 7.4 - + - -
446A GLN* 5.6 0.6 + - - -
450A PHE* 4.2 5.0 - + - -
548A GLU* 3.6 22.8 - - - +
602A ASP* 2.6 35.5 + - - -
603A ARG* 3.2 47.8 - - + +
643A ASP* 3.4 12.3 - - - -
644A THR* 3.3 11.6 + - - -
645A ALA* 3.3 33.1 - - + +
665A CYS* 3.0 11.7 + - - -
666A PRO* 1.3 74.0 - - - +
668A LEU* 1.3 75.0 + - + +
670A LEU* 3.6 7.8 + - - +
671A GLU* 3.0 27.0 + - - +
674A ARG* 4.5 0.7 + - - -
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Residues in contact with LEU 668 (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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437A PHE* 3.8 26.9 - - + -
443A VAL* 4.6 5.2 - - + -
446A GLN* 3.7 39.7 - - + +
447A GLN* 3.7 11.2 - - + +
450A PHE* 6.0 0.2 - - + -
452A TYR* 3.4 31.2 - - + +
645A ALA* 3.7 28.5 - - + +
666A PRO 3.4 0.4 - - - -
667A TYR* 1.3 87.5 - - + +
669A ALA* 1.3 54.2 + - - +
671A GLU* 3.9 8.5 - - + -
672A SER* 2.7 44.5 + - - +
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Residues in contact with ALA 669 (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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452A TYR* 3.2 11.7 + - - +
461A VAL* 4.5 2.6 - - + +
645A ALA 4.9 0.2 + - - -
647A CYS 3.4 24.2 + - - +
648A TRP* 3.9 6.5 - - + -
666A PRO* 3.1 10.5 + - + +
668A LEU* 1.3 74.5 - - - +
670A LEU* 1.3 65.1 + - - +
672A SER* 3.1 9.3 + - - -
673A VAL* 3.0 27.1 + - - +
703A TYR* 3.4 26.7 - - + +
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Residues in contact with LEU 670 (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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431A PHE* 4.4 15.9 - - + -
545A LEU* 4.7 4.9 - - + -
546A VAL 4.6 0.4 - - - +
547A ASN* 4.1 29.4 - - + -
548A GLU* 4.5 6.3 - - + +
665A CYS* 5.0 1.1 - - - -
666A PRO* 3.1 29.0 + - + +
667A TYR* 3.8 10.1 - - - +
669A ALA* 1.3 76.1 - - - +
671A GLU* 1.3 56.4 + - - +
673A VAL* 3.2 6.4 + - - +
674A ARG* 2.9 53.1 + - - +
700A LEU* 3.9 19.4 - - + +
703A TYR* 3.8 28.7 - - + -
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Residues in contact with GLU 671 (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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435A THR* 3.5 6.2 - - - -
436A LEU* 2.9 28.4 + - + +
437A PHE* 3.2 38.4 + - + -
443A VAL* 4.5 1.6 - - + -
667A TYR 3.0 19.0 + - - +
668A LEU* 3.7 13.5 - - + +
669A ALA 3.3 0.2 - - - -
670A LEU* 1.3 76.2 - - - +
672A SER* 1.3 57.7 + - - +
674A ARG* 2.8 34.2 + - - +
675A GLN* 2.9 59.7 + - + +
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Residues in contact with SER 672 (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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443A VAL* 5.1 0.9 - - - -
447A GLN* 2.9 31.8 + - - +
452A TYR* 3.7 15.9 - - - -
457A VAL* 5.5 6.7 - - - +
461A VAL* 4.4 14.4 - - - -
668A LEU* 2.7 24.9 + - - +
669A ALA* 3.1 12.5 + - - -
671A GLU* 1.3 73.2 - - - +
673A VAL* 1.3 56.8 + - - +
675A GLN* 3.4 4.3 + - - +
676A TRP* 3.0 30.0 + - - +
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Residues in contact with VAL 673 (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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461A VAL* 3.7 21.3 - - + -
465A ALA* 3.8 28.9 - - + -
669A ALA 3.0 14.7 + - - +
670A LEU* 3.5 8.3 - - - +
672A SER* 1.3 71.8 - - - +
674A ARG* 1.3 68.1 + - - +
676A TRP* 3.2 8.7 + - + +
677A TRP* 3.0 23.0 + - - +
696A LEU* 5.0 0.9 - - + -
699A ALA* 4.0 21.1 - - + +
700A LEU* 3.9 20.2 - - + -
703A TYR* 4.0 18.6 - - + -
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Residues in contact with ARG 674 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A PHE* 5.8 2.0 - - - +
432A ALA* 2.9 28.2 + - - +
433A GLU 3.6 20.6 - - - +
434A LYS 3.7 11.8 + - - -
435A THR* 4.2 11.4 - - + +
436A LEU* 4.1 13.1 - - - +
548A GLU* 3.8 26.4 + - - +
667A TYR 4.5 1.2 + - - -
670A LEU* 2.9 33.5 + - - +
671A GLU* 2.8 56.2 + - - +
673A VAL* 1.3 77.8 - - - +
675A GLN* 1.3 56.9 + - - +
677A TRP* 3.4 1.9 + - - +
678A LEU* 2.8 38.4 + - + +
696A LEU* 4.0 16.6 - - + -
700A LEU* 4.3 13.4 - - + +
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Residues in contact with GLN 675 (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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435A THR* 3.6 15.9 - - - +
437A PHE 3.5 16.6 + - - -
438A ASN* 5.5 2.0 - - - +
439A ASP 5.4 0.4 + - - -
440A ALA* 4.6 13.8 - - + +
443A VAL* 3.7 35.7 - - + +
447A GLN* 5.9 0.4 - - - +
671A GLU* 2.9 42.3 + - - +
672A SER* 4.0 3.4 - - - +
674A ARG* 1.3 74.0 - - - +
676A TRP* 1.3 61.3 + - - +
678A LEU* 2.5 36.3 - - - +
679A ASP* 3.4 7.6 - - - +
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Residues in contact with TRP 676 (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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457A VAL* 6.0 2.7 - - + -
461A VAL* 6.5 0.4 - - + -
462A VAL* 3.4 42.4 - - + +
465A ALA* 4.2 17.3 - - + -
466A SER* 3.7 25.8 - - - -
672A SER 3.0 17.9 + - - +
673A VAL* 3.2 10.3 + - + +
675A GLN* 1.3 74.6 - - - +
677A TRP* 1.3 84.9 + + + +
679A ASP* 3.3 9.2 - - + +
682A THR* 2.6 55.3 + - + -
686A MET* 5.6 4.5 - - - -
690A ARG* 2.8 38.0 - - + +
691A LEU 6.2 0.2 - - - -
694A ILE* 5.3 5.4 - - + -
699A ALA* 4.2 22.4 - - + -
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Residues in contact with TRP 677 (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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673A VAL 3.0 15.9 + - - +
674A ARG 3.7 2.7 - - - +
676A TRP* 1.3 93.5 - + + +
678A LEU* 1.3 82.5 + - + +
679A ASP 3.2 5.2 + - - +
682A THR* 4.0 7.8 - - - +
683A GLN* 2.9 54.7 + - - +
686A MET* 4.1 18.8 - - + +
694A ILE* 2.9 25.2 + - + -
695A ASP* 3.4 21.3 - - + -
696A LEU* 3.5 42.6 - - + -
699A ALA* 4.3 10.8 - - + -
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Residues in contact with LEU 678 (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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433A GLU 5.0 2.0 - - - +
435A THR* 3.4 32.3 - - + -
674A ARG* 2.8 28.9 + - + +
675A GLN* 2.5 30.3 - - - +
677A TRP* 1.3 94.1 - - + +
679A ASP* 1.3 54.2 + - - +
683A GLN* 4.4 5.2 - - - +
696A LEU* 4.8 9.0 - - + -
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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