Contacts of the helix formed by residues 649 - 659 (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 SER 649 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460B VAL* 4.2 17.0 - - - -
464B MET* 4.6 0.9 - - - -
648B TRP* 1.3 94.7 - - - +
650B THR* 1.3 67.1 + - - +
651B HIS* 3.7 8.1 + - - +
652B HIS* 3.0 41.6 + - - +
653B PHE* 3.0 19.2 - - - -
707B VAL* 5.4 0.2 - - - -
1071B SER* 6.5 1.1 - - - -
1075B HIS* 4.9 4.7 + - - -
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Residues in contact with THR 650 (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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460B VAL* 5.7 0.2 - - - +
464B MET* 5.1 6.7 - - - -
470B GLU* 4.0 27.2 + - - +
648B TRP 4.2 0.2 + - - -
649B SER* 1.3 73.9 - - - +
651B HIS* 1.3 63.9 + - - +
653B PHE* 3.4 8.5 + - - +
654B ALA* 3.2 21.5 + - - +
706B SER 3.9 9.0 + - - -
707B VAL* 4.3 10.4 + - - +
710B GLY* 3.4 31.4 - - - +
711B LEU* 4.2 3.5 - - - +
713B LYS* 6.1 0.2 - - + -
714B ILE* 3.3 24.0 - - + +
1071B SER* 4.3 11.2 - - - +
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Residues in contact with HIS 651 (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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492B TYR* 3.0 36.2 + - - +
495B PHE 3.1 19.0 + - - -
497B GLN* 3.1 34.6 - - + +
649B SER* 3.7 5.3 + - - +
650B THR* 1.3 81.4 - - + +
652B HIS* 1.3 57.6 + - - +
654B ALA* 3.4 1.8 + - - +
655B CYS* 2.9 47.6 + - - -
714B ILE* 4.1 8.3 - - + -
732B PHE* 3.9 8.4 - + - -
1071B SER* 5.3 1.9 - - - -
1075B HIS* 3.5 47.0 + + + +
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Residues in contact with HIS 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B LEU* 3.7 14.2 - - + +
492B TYR* 3.2 56.4 - + + +
493B ASP* 5.0 6.5 - - - -
647B CYS* 3.7 20.4 - - - -
648B TRP* 3.2 47.2 + + - -
649B SER* 3.0 28.5 + - - +
651B HIS* 1.3 80.4 + - - +
653B PHE* 1.3 64.1 + - - +
655B CYS 3.3 1.2 + - - -
656B LEU* 3.0 23.8 + - - +
1075B HIS* 5.5 3.1 - + - -
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Residues in contact with PHE 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B PRO* 5.7 0.9 - - + -
545B LEU* 3.9 19.3 - - + -
647B CYS* 3.8 17.5 - - - -
648B TRP 3.9 3.1 - - - -
649B SER 3.0 27.3 + - - -
650B THR 3.9 4.0 - - - +
652B HIS* 1.3 79.1 - - - +
654B ALA* 1.3 61.7 - - - +
656B LEU* 3.5 5.4 + - - +
657B VAL* 3.1 30.8 + - + +
664B ILE* 3.6 26.2 - - + -
666B PRO* 3.6 37.0 - - + -
703B TYR* 3.6 21.3 - - - -
707B VAL* 3.6 35.0 - - + -
711B LEU* 4.1 17.5 - - + -
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Residues in contact with ALA 654 (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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650B THR 3.2 11.5 + - - +
651B HIS* 3.6 9.0 - - + +
653B PHE* 1.3 77.1 - - - +
655B CYS* 1.3 59.8 + - - +
657B VAL* 3.9 0.6 - - - -
658B GLY* 2.8 26.9 + - - -
711B LEU* 3.7 14.0 - - + +
714B ILE* 3.7 22.4 - - + -
726B TYR* 3.4 30.9 - - + +
732B PHE* 3.8 7.5 - - + -
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Residues in contact with CYS 655 (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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492B TYR* 3.6 19.7 - - + -
495B PHE* 4.1 14.6 - - - -
619B LEU* 4.0 14.6 - - + -
651B HIS* 2.9 51.6 + - - +
652B HIS 3.6 4.3 - - - +
654B ALA* 1.3 74.1 - - - +
656B LEU* 1.3 64.9 - - - +
658B GLY 3.2 0.9 + - - -
659B TYR* 3.0 30.6 + - + +
732B PHE* 3.6 19.7 - - - -
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Residues in contact with LEU 656 (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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492B TYR* 3.2 32.8 - - + +
618B PRO* 3.8 8.3 - - + +
619B LEU* 3.5 34.8 - - - +
622B VAL* 4.0 7.5 - - + +
642B VAL* 4.0 26.2 - - + -
647B CYS* 3.7 23.1 - - + -
652B HIS 3.0 17.4 + - - +
653B PHE 3.8 1.3 - - - +
654B ALA 3.3 0.2 - - - -
655B CYS* 1.3 78.0 - - - +
657B VAL* 1.3 60.1 + - - +
659B TYR* 3.4 3.1 + - - -
660B GLY 3.2 6.4 + - - -
661B ALA* 3.0 24.1 + - + +
664B ILE* 3.8 17.3 - - + -
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Residues in contact with VAL 657 (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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520B MET* 4.4 2.0 - - + -
544B PRO* 4.4 20.9 - - + -
653B PHE* 3.1 18.8 + - + +
654B ALA* 4.0 3.1 - - - +
656B LEU* 1.3 73.6 - - - +
658B GLY* 1.3 57.4 + - - +
660B GLY 3.1 7.8 + - - -
661B ALA 3.4 21.5 - - - +
662B SER 5.2 1.3 - - - +
664B ILE* 4.3 13.5 - - + -
711B LEU* 5.6 1.6 - - + -
723B LEU* 3.8 32.8 - - + -
726B TYR* 4.1 4.3 - - + -
727B HIS* 2.7 49.9 + - + +
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Residues in contact with GLY 658 (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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626B HIS* 5.6 0.3 + - - -
654B ALA 2.8 20.7 + - - -
655B CYS 3.6 2.0 - - - -
657B VAL* 1.3 74.0 - - - +
659B TYR* 1.3 62.1 + - - +
726B TYR* 3.9 14.3 - - - -
727B HIS 3.1 9.8 - - - +
728B GLY 3.7 1.7 - - - -
729B ALA 2.6 30.1 - - - +
730B GLN* 3.6 7.4 - - - +
732B PHE* 4.3 9.0 - - - -
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Residues in contact with TYR 659 (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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495B PHE* 3.6 23.1 - + - -
619B LEU* 4.0 20.0 - - + -
622B VAL* 3.8 4.4 - - + +
623B GLY* 3.7 18.0 + - - -
626B HIS* 3.4 24.8 - - - +
627B HIS* 4.8 0.7 - - - -
655B CYS* 3.0 22.9 + - - +
656B LEU 3.6 5.2 - - - +
658B GLY* 1.3 77.9 - - - +
660B GLY* 1.3 54.2 + - - +
730B GLN* 3.4 36.9 + - + +
732B PHE* 3.7 30.5 - + - +
745B ALA 4.3 2.5 - - - -
746B PHE* 3.7 26.0 - + + -
749B THR* 2.6 42.4 + - - +
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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