Contacts of the helix formed by residues 649 - 659 (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 SER 649 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460A VAL* 4.4 15.5 - - - -
464A MET* 4.8 1.1 - - - -
648A TRP* 1.3 89.2 - - - +
650A THR* 1.3 59.6 + - - +
651A HIS* 3.6 7.9 + - - +
652A HIS* 3.0 55.8 + - - +
653A PHE* 3.0 20.4 - - - -
707A VAL* 5.5 0.2 - - - -
1071A SER* 6.3 2.2 - - - -
1075A HIS* 5.0 4.6 + - - -
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Residues in contact with THR 650 (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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464A MET* 5.2 6.6 - - - -
470A GLU* 3.9 33.0 + - - +
648A TRP 4.2 0.2 + - - -
649A SER* 1.3 72.4 - - - +
651A HIS* 1.3 62.9 + - - +
652A HIS 3.4 0.2 + - - -
653A PHE* 3.4 10.1 + - - +
654A ALA* 3.2 22.0 + - - +
706A SER 3.9 8.8 + - - -
707A VAL* 4.1 10.2 + - - +
710A GLY* 3.3 25.6 - - - +
711A LEU* 4.1 3.6 - - - +
713A LYS* 6.1 0.2 - - + -
714A ILE* 3.6 22.8 - - + +
1071A SER* 4.1 13.9 - - - +
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Residues in contact with HIS 651 (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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492A TYR* 3.0 35.7 + - - +
495A PHE 3.1 20.1 + - - -
497A GLN* 3.0 34.3 - - + +
649A SER* 3.3 7.9 + - - +
650A THR* 1.3 80.6 - - + +
652A HIS* 1.3 63.2 + - - +
654A ALA* 3.4 1.6 + - - +
655A CYS* 3.0 43.3 + - - -
714A ILE* 4.1 7.6 - - - -
732A PHE* 3.9 7.8 - + - -
1071A SER* 5.3 1.3 - - - -
1075A HIS* 3.4 46.1 + + + +
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Residues in contact with HIS 652 (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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490A LEU* 3.8 14.3 - - + +
492A TYR* 3.2 53.0 - + + +
493A ASP* 5.2 4.9 - - - -
647A CYS* 3.6 23.1 - - - -
648A TRP* 3.0 49.3 + + - -
649A SER* 3.0 30.9 + - - +
651A HIS* 1.3 78.8 + - - +
653A PHE* 1.3 61.7 + - - +
655A CYS 3.3 0.7 + - - -
656A LEU* 3.0 24.8 + - - +
1075A HIS* 5.5 2.9 - - - -
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Residues in contact with PHE 653 (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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544A PRO* 5.9 1.3 - - + -
545A LEU* 4.0 17.5 - - + -
647A CYS* 3.8 18.6 - - - -
648A TRP 3.9 4.0 - - - -
649A SER 3.0 27.6 + - - -
650A THR* 3.8 6.1 - - - +
651A HIS 3.4 0.4 - - - -
652A HIS* 1.3 78.3 - - - +
654A ALA* 1.3 62.6 + - - +
656A LEU* 3.4 5.5 + - - +
657A VAL* 3.1 28.9 + - + +
664A ILE* 3.6 26.9 - - + +
666A PRO* 3.7 37.0 - - + -
703A TYR* 3.6 15.0 - - - -
707A VAL* 3.6 39.3 - - + -
711A LEU* 4.1 17.7 - - + -
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Residues in contact with ALA 654 (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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497A GLN* 5.4 0.2 - - - +
650A THR 3.2 14.6 + - - +
651A HIS* 3.7 4.7 - - - +
652A HIS 3.2 0.2 - - - -
653A PHE* 1.3 77.2 - - - +
655A CYS* 1.3 59.4 + - - +
657A VAL* 3.5 1.5 + - - -
658A GLY* 2.8 26.7 + - - -
711A LEU* 3.7 13.6 - - + +
714A ILE* 3.8 22.0 - - + -
726A TYR* 3.3 30.2 - - + +
732A PHE* 3.7 6.4 - - + -
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Residues in contact with CYS 655 (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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492A TYR* 3.7 26.0 - - + -
495A PHE* 4.2 12.8 - - - -
619A LEU* 3.9 14.4 - - + -
651A HIS* 3.0 54.7 + - - +
652A HIS 3.7 0.2 - - - +
654A ALA* 1.3 75.1 - - - +
656A LEU* 1.3 66.5 + - - +
658A GLY 3.3 0.9 + - - -
659A TYR* 3.0 30.6 + - + +
732A PHE* 3.6 19.9 - - - -
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Residues in contact with LEU 656 (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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492A TYR* 3.5 30.3 - - + +
618A PRO* 3.9 8.1 - - + +
619A LEU* 3.6 34.1 - - + +
622A VAL* 3.9 7.8 - - + +
642A VAL* 3.8 19.1 - - + -
644A THR* 4.6 0.4 - - + -
647A CYS* 3.6 27.4 - - + -
652A HIS 3.0 12.0 + - - +
653A PHE 3.6 4.3 - - - +
654A ALA 3.3 0.2 - - - -
655A CYS* 1.3 78.7 - - - +
657A VAL* 1.3 61.3 + - - +
659A TYR 3.4 2.6 + - - -
660A GLY 3.3 5.5 + - - -
661A ALA* 3.0 22.9 + - + +
664A ILE* 3.6 27.4 - - + -
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Residues in contact with VAL 657 (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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520A MET* 4.2 1.8 - - + -
544A PRO* 4.5 19.5 - - + -
653A PHE* 3.1 18.2 + - + +
654A ALA* 4.0 2.9 - - - +
656A LEU* 1.3 75.5 - - - +
658A GLY* 1.3 59.8 + - - +
660A GLY 3.0 8.5 + - - -
661A ALA 3.4 20.9 - - - +
662A SER 5.1 1.3 - - - +
664A ILE* 4.1 14.8 - - + -
711A LEU* 5.6 2.2 - - + -
723A LEU* 3.8 34.1 - - + -
726A TYR* 4.1 2.9 - - + -
727A HIS* 2.8 44.6 + - + +
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Residues in contact with GLY 658 (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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626A HIS* 5.7 0.3 + - - -
654A ALA 2.8 21.3 + - - -
655A CYS 3.7 1.6 - - - -
657A VAL* 1.3 73.8 - - - +
659A TYR* 1.3 61.5 + - - +
660A GLY 3.5 0.2 - - - -
726A TYR* 3.9 16.5 - - - -
727A HIS 3.3 7.3 - - - +
728A GLY 3.9 1.4 - - - +
729A ALA 2.6 29.1 + - - +
730A GLN* 3.5 8.3 - - - +
732A PHE* 4.3 8.3 - - - -
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Residues in contact with TYR 659 (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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495A PHE* 3.5 25.0 - + - -
619A LEU* 4.0 20.2 - - + -
622A VAL* 3.7 11.0 - - + +
623A GLY* 3.7 11.1 - - - -
626A HIS* 3.4 24.8 - - - +
627A HIS* 4.9 0.7 - + - -
655A CYS* 3.0 29.1 + - - +
656A LEU 3.6 4.5 - - - +
657A VAL 3.1 0.2 - - - -
658A GLY* 1.3 79.9 - - - +
660A GLY* 1.3 55.7 + - - -
730A GLN* 3.3 36.1 + - + +
732A PHE* 3.6 28.4 - + - +
745A ALA 4.3 2.2 - - - -
746A PHE* 3.7 24.9 - + + -
749A THR* 2.7 41.0 + - - +
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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