Contacts of the helix formed by residues 657 - 675 (chain u) in PDB entry 6FF7
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 657 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654u SER 4.5 6.9 - - - +
655u LYS* 5.3 0.6 - - - -
656u LYS* 1.3 82.3 + - - +
658u TRP* 1.3 63.1 + - - +
659u GLN* 3.2 13.6 + - - -
660u ALA* 3.7 16.2 + - - +
661u ARG* 4.3 3.1 + - - +
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Residues in contact with TRP 658 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657u SER* 1.3 71.8 - - - +
659u GLN* 1.3 59.5 + - - +
660u ALA 3.3 0.7 - - - -
661u ARG* 3.5 8.2 + - + +
662u HIS* 2.9 29.9 + - - +
698u GLN* 4.5 21.5 - - + -
701u VAL* 5.3 7.8 - - + +
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Residues in contact with GLN 659 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617u ILE 4.4 15.8 - - - +
618u ASP* 5.4 4.7 - - - -
619u ASN 5.6 3.8 - - - +
657u SER* 3.2 9.7 - - - -
658u TRP* 1.3 79.1 - - - +
660u ALA* 1.3 56.4 + - - +
662u HIS* 3.6 7.2 - - - +
663u THR* 2.9 29.1 + - - -
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Residues in contact with ALA 660 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617u ILE* 5.1 12.0 + - + -
618u ASP* 6.2 1.1 - - - +
651u VAL* 3.4 24.4 - - + +
654u SER* 5.4 9.6 - - - +
657u SER* 3.7 12.2 + - - +
658u TRP 3.3 0.2 - - - -
659u GLN* 1.3 76.1 - - - +
661u ARG* 1.3 59.8 + - - +
663u THR* 3.3 7.6 + - - -
664u GLY* 2.9 23.7 + - - -
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Residues in contact with ARG 661 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651u VAL 3.7 10.0 + - - +
652u CYS* 4.0 22.6 - - + +
654u SER 4.9 8.4 + - - +
657u SER 4.3 1.7 + - - +
658u TRP* 3.5 13.0 + - - +
660u ALA* 1.3 74.9 - - - +
662u HIS* 1.3 60.4 + - - +
665u ILE* 3.0 31.9 + - - +
701u VAL* 5.6 9.0 - - + -
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Residues in contact with HIS 662 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658u TRP 2.9 19.1 + - - +
659u GLN* 3.6 9.4 - - - +
661u ARG* 1.3 76.9 - - - +
663u THR* 1.3 56.8 + - - +
665u ILE* 3.6 4.1 + - - +
666u LYS* 2.9 29.9 + - - +
700u LYS* 5.9 4.9 - - + +
701u VAL* 5.4 16.0 - - + +
704u ILE* 5.2 9.3 - - + +
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Residues in contact with THR 663 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617u ILE* 4.8 18.8 - - - -
625u ARG* 5.3 9.9 - - - -
629u ALA* 3.9 12.7 - - - +
651u VAL* 6.4 0.4 - - - -
659u GLN 2.9 18.7 + - - -
660u ALA* 3.5 8.1 - - - -
661u ARG 3.3 0.2 - - - -
662u HIS* 1.3 75.9 - - - +
664u GLY* 1.3 57.1 + - - +
666u LYS* 3.2 8.3 + - - +
667u ILE* 2.9 26.7 + - - +
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Residues in contact with GLY 664 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648u LEU* 5.3 11.4 - - - +
651u VAL* 4.9 12.7 - - - +
652u CYS* 5.1 11.2 - - - -
660u ALA 2.9 15.3 + - - -
661u ARG 3.9 1.1 - - - -
663u THR* 1.3 74.0 - - - +
665u ILE* 1.3 60.1 + - - +
667u ILE* 3.2 10.1 + - - +
668u VAL* 3.0 25.5 + - - +
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Residues in contact with ILE 665 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652u CYS* 5.2 3.6 - - + +
661u ARG 3.0 17.2 + - - +
662u HIS* 4.1 4.7 - - - +
664u GLY* 1.3 76.1 - - - +
666u LYS* 1.3 58.2 + - - +
668u VAL* 3.3 9.8 + - - +
669u GLN* 2.9 27.2 + - - +
701u VAL* 5.5 1.8 - - - +
704u ILE* 4.7 22.0 - - + +
705u SER* 4.9 8.7 - - - +
708u ALA* 4.0 8.0 - - + +
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Residues in contact with LYS 666 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626u ASN* 6.0 2.5 - - - -
629u ALA* 4.0 16.0 - - + +
662u HIS 2.9 20.1 + - - +
663u THR* 3.3 8.1 - - - +
665u ILE* 1.3 74.8 - - - +
667u ILE* 1.3 59.2 + - - +
669u GLN* 3.3 7.8 + - - +
670u GLN* 2.9 31.0 + - - +
704u ILE* 5.5 4.7 - - + +
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Residues in contact with ILE 667 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629u ALA* 4.1 20.8 - - + +
632u PHE* 4.5 14.6 - - + -
633u ALA* 4.1 5.5 - - - +
648u LEU* 5.7 7.4 - - + -
663u THR 2.9 12.7 + - - +
664u GLY* 3.2 13.4 + - - +
666u LYS* 1.3 76.5 - - - +
668u VAL* 1.3 56.4 + - - +
670u GLN* 3.4 0.9 + - - -
671u ILE* 2.9 31.5 + - - +
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Residues in contact with VAL 668 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648u LEU* 6.3 2.0 - - + +
664u GLY 3.0 12.2 + - - +
665u ILE* 3.3 12.8 + - - +
667u ILE* 1.3 75.0 - - - +
669u GLN* 1.3 57.5 + - - +
671u ILE* 3.4 5.8 + - - +
672u ALA* 2.9 31.2 + - - +
686u LEU* 6.0 4.5 - - + +
708u ALA* 4.6 11.0 - - + -
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Residues in contact with GLN 669 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665u ILE 2.9 16.3 + - - +
666u LYS* 3.6 9.6 - - - +
667u ILE 3.2 0.4 - - - -
668u VAL* 1.3 76.4 - - - +
670u GLN* 1.3 57.0 + - - +
672u ALA* 3.2 3.3 + - - +
673u ILE* 2.9 29.3 + - - +
704u ILE 5.3 2.2 - - - +
707u LEU* 4.9 5.4 - - + +
708u ALA* 4.3 17.9 - - + +
711u ALA* 4.0 15.1 - - + +
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Residues in contact with GLN 670 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629u ALA 5.0 0.2 - - - +
630u ARG* 4.6 14.4 - - + +
633u ALA* 3.7 20.9 - - + +
666u LYS 2.9 15.8 + - - +
669u GLN* 1.3 74.1 - - - +
671u ILE* 1.3 60.8 + - - +
673u ILE* 4.4 4.5 - - - +
674u LEU* 2.8 33.0 + - + +
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Residues in contact with ILE 671 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633u ALA* 3.7 16.4 - - + +
636u ALA* 5.4 7.4 - - + -
637u SER* 6.5 0.2 - - - -
667u ILE 2.9 18.7 + - - +
668u VAL* 3.7 6.7 - - - +
670u GLN* 1.3 76.8 - - - +
672u ALA* 1.3 61.1 + - - +
674u LEU* 4.4 2.9 - - - -
675u MET* 3.2 28.1 + - - +
679u ILE* 5.1 5.6 - - + +
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Residues in contact with ALA 672 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668u VAL 2.9 17.9 + - - +
669u GLN* 3.2 0.4 + - - -
671u ILE* 1.3 76.3 - - - +
673u ILE* 1.3 60.0 + - - +
675u MET 3.4 14.5 - - - +
676u GLY* 5.0 0.7 - - - -
679u ILE* 5.3 6.3 - - + -
708u ALA 5.0 0.9 - - - +
711u ALA* 3.7 36.1 - - + +
712u LEU* 3.9 10.8 - - + +
715u ALA* 3.4 20.2 - - + +
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Residues in contact with ILE 673 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669u GLN 2.9 16.2 + - - +
670u GLN* 4.6 4.0 - - - +
672u ALA* 1.3 76.1 - - - +
674u LEU* 1.3 63.8 + - - +
675u MET 4.9 0.4 - - - -
711u ALA* 5.0 6.7 - - + -
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Residues in contact with LEU 674 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633u ALA* 5.3 7.0 - - + +
634u VAL* 6.1 1.3 - - - -
637u SER* 5.3 9.4 - - - -
670u GLN* 2.8 22.1 + - + +
671u ILE* 3.3 4.9 + - - +
673u ILE* 1.3 81.6 - - - +
675u MET* 1.3 62.1 + - + +
676u GLY 4.1 1.2 + - - -
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Residues in contact with MET 675 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637u SER* 4.8 18.2 - - - -
671u ILE 3.2 11.5 + - - +
672u ALA 3.4 14.2 - - - +
673u ILE 5.1 0.2 - - - -
674u LEU* 1.3 77.7 - - + +
676u GLY* 1.3 66.3 + - - +
677u CYS 4.0 0.4 - - - -
678u ALA* 5.1 11.7 - - + -
679u ILE* 4.4 12.8 - - + +
715u ALA* 4.6 0.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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