Contacts of the helix formed by residues 698 - 717 (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 GLN 698 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658u TRP* 4.5 18.6 - - + -
696u ASP* 3.2 8.5 - - + +
697u GLU* 1.3 79.5 - - - +
699u GLN* 1.3 63.9 + - - +
700u LYS* 4.3 4.3 - - + +
701u VAL* 4.1 21.9 - - + +
702u ARG* 3.4 20.1 + - - +
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Residues in contact with GLN 699 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697u GLU 4.1 1.2 + - - -
698u GLN* 1.3 71.0 - - - +
700u LYS* 1.3 60.6 + - - +
702u ARG* 3.5 5.3 + - - +
703u THR* 2.9 31.3 + - - -
742u GLY* 6.0 0.7 - - - -
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Residues in contact with LYS 700 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662u HIS* 5.9 2.0 - - - +
698u GLN* 3.4 4.4 - - + +
699u GLN* 1.3 79.9 - - - +
701u VAL* 1.3 57.1 + - - +
703u THR* 3.4 5.5 + - - -
704u ILE* 2.9 31.7 + - - +
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Residues in contact with VAL 701 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658u TRP* 5.3 12.6 - - + +
661u ARG* 5.6 6.7 - - + -
662u HIS* 5.4 13.9 - - + +
665u ILE* 5.5 2.1 - - - +
693u GLY* 6.5 0.2 - - - -
694u LEU 5.7 0.9 - - - -
696u ASP* 4.7 13.7 - - + -
698u GLN* 3.7 21.0 + - + +
699u GLN 3.3 0.2 - - - -
700u LYS* 1.3 79.4 - - - +
702u ARG* 1.3 56.7 + - - +
704u ILE* 3.5 3.7 + - - +
705u SER* 2.9 31.3 + - - -
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Residues in contact with ARG 702 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694u LEU* 4.4 25.8 - - - +
696u ASP* 5.4 6.1 - - + +
698u GLN 3.4 14.0 + - - +
699u GLN* 3.9 6.5 - - - +
700u LYS 3.4 0.6 - - - -
701u VAL* 1.3 77.9 - - - +
703u THR* 1.3 57.4 + - - +
705u SER* 3.3 7.2 + - - -
706u ALA* 3.0 28.6 + - - +
742u GLY* 6.3 0.2 - - - -
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Residues in contact with THR 703 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699u GLN 2.9 18.4 + - - -
700u LYS* 3.7 7.6 - - - -
702u ARG* 1.3 77.4 - - - +
704u ILE* 1.3 57.9 + - - +
706u ALA* 3.3 4.7 + - - +
707u LEU* 2.9 26.2 + - - +
741u LYS* 5.2 4.9 - - - -
742u GLY* 5.1 11.9 - - - -
745u ALA* 3.8 20.3 - - - +
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Residues in contact with ILE 704 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662u HIS* 5.2 10.3 - - + +
665u ILE* 4.7 15.6 - - + +
666u LYS* 5.5 5.8 - - + +
669u GLN* 5.3 1.7 - - - +
700u LYS 2.9 18.0 + - - +
701u VAL* 4.3 3.1 - - - +
703u THR* 1.3 73.9 - - - +
705u SER* 1.3 60.3 + - - +
707u LEU* 3.6 8.4 - - + +
708u ALA* 2.9 28.4 + - - +
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Residues in contact with SER 705 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665u ILE* 4.9 9.3 - - - +
690u ILE* 5.0 16.5 - - - +
693u GLY* 5.1 2.7 - - - -
694u LEU* 4.4 18.4 - - - -
701u VAL 2.9 19.1 + - - -
702u ARG* 3.6 7.9 - - - -
704u ILE* 1.3 75.6 - - - +
706u ALA* 1.3 60.3 + - - +
708u ALA* 3.2 6.9 + - - +
709u ILE* 2.9 28.2 + - - +
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Residues in contact with ALA 706 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702u ARG 3.0 17.1 + - - +
703u THR 3.3 4.9 + - - +
705u SER* 1.3 77.0 - - - +
707u LEU* 1.3 55.8 + - - +
709u ILE* 3.4 5.7 + - - -
710u ALA* 2.9 29.3 + - - +
742u GLY 5.5 0.4 - - - +
745u ALA* 3.6 32.3 - - + +
746u PHE* 4.0 7.6 - - + +
749u ALA* 3.5 9.8 - - + +
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Residues in contact with LEU 707 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669u GLN* 4.9 7.0 - - + +
703u THR 2.9 17.1 + - - +
704u ILE* 3.6 11.0 - - + +
705u SER 3.3 0.2 - - - -
706u ALA* 1.3 76.2 - - - +
708u ALA* 1.3 57.7 + - - +
710u ALA* 3.4 7.8 + - - +
711u ALA* 2.9 28.6 + - - +
745u ALA* 4.8 4.7 - - + +
748u LYS* 6.4 0.4 - - - -
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Residues in contact with ALA 708 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665u ILE* 4.0 22.4 - - + +
668u VAL* 4.6 8.7 - - + +
669u GLN* 4.3 11.1 - - + +
672u ALA* 5.0 1.4 - - - +
690u ILE* 5.8 6.5 - - + -
704u ILE 2.9 16.8 + - - +
705u SER* 3.2 8.5 + - - +
707u LEU* 1.3 75.0 - - - +
709u ILE* 1.3 60.0 + - - +
711u ALA* 3.7 7.0 - - - +
712u LEU* 2.9 29.5 + - - +
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Residues in contact with ILE 709 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690u ILE* 6.1 5.3 - - + +
705u SER 2.9 16.3 + - - +
706u ALA* 3.8 6.5 - - - +
708u ALA* 1.3 75.2 - - - +
710u ALA* 1.3 57.0 + - - +
712u LEU* 3.4 5.8 + - - +
713u ALA* 2.9 30.3 + - - +
727u VAL* 5.6 9.9 - - + -
749u ALA* 4.4 12.1 - - + -
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Residues in contact with ALA 710 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706u ALA 2.9 17.5 + - - +
707u LEU* 3.6 9.4 - - - +
708u ALA 3.3 0.2 - - - -
709u ILE* 1.3 76.8 - - - +
711u ALA* 1.3 56.3 + - - +
713u ALA* 3.4 2.0 + - - +
714u GLU* 2.9 29.6 + - - +
748u LYS* 4.1 13.7 - - + +
749u ALA* 3.8 26.3 - - - +
752u TYR* 3.9 10.1 - - + +
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Residues in contact with ALA 711 (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* 4.0 14.6 - - + +
672u ALA* 3.7 20.9 - - + +
673u ILE* 4.7 8.5 - - + +
707u LEU 2.9 17.7 + - - +
708u ALA* 3.7 8.3 - - - +
709u ILE 3.3 0.4 - - - -
710u ALA* 1.3 74.6 - - - +
712u LEU* 1.3 59.1 + - - +
714u GLU* 3.3 7.1 + - - +
715u ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 712 (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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672u ALA* 3.9 11.3 - - + +
687u VAL* 6.1 5.4 - - + -
708u ALA 2.9 18.4 + - - +
709u ILE* 3.8 6.1 - - - +
711u ALA* 1.3 75.7 - - - +
713u ALA* 1.3 58.1 + - - +
715u ALA* 3.7 3.7 - - - +
716u ALA* 2.9 30.8 + - - +
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Residues in contact with ALA 713 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709u ILE 2.9 18.3 + - - +
710u ALA* 3.7 4.9 - - - +
712u LEU* 1.3 73.5 - - - +
714u GLU* 1.3 65.1 + - - +
716u ALA* 3.7 9.5 + - - +
717u THR* 3.8 11.8 + - - -
749u ALA 4.8 0.9 - - - +
752u TYR* 3.5 37.3 - - + +
753u LEU* 3.9 10.8 - - + +
756u LEU* 6.0 3.6 - - + +
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Residues in contact with GLU 714 (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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710u ALA 2.9 17.9 + - - +
711u ALA* 3.7 7.2 - - - +
712u LEU 3.3 0.2 - - - -
713u ALA* 1.3 77.7 - - - +
715u ALA* 1.3 60.4 - - - +
717u THR* 3.9 12.1 - - - -
752u TYR* 4.5 6.7 - - + +
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Residues in contact with ALA 715 (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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672u ALA* 3.4 24.9 + - + +
675u MET 4.6 0.4 - - - +
676u GLY* 3.0 35.1 - - - +
677u CYS* 4.3 4.9 - - - +
679u ILE* 5.4 6.5 - - + -
680u LEU* 5.7 0.6 - - - +
711u ALA 2.9 17.3 + - - +
712u LEU* 3.7 7.2 - - - +
713u ALA 3.3 0.4 - - - -
714u GLU* 1.3 77.9 - - - +
716u ALA* 1.3 66.4 + - - +
717u THR* 4.4 1.7 - - - -
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Residues in contact with ALA 716 (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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677u CYS* 5.3 5.7 - - - +
680u LEU* 5.2 15.4 - - + +
712u LEU 2.9 17.6 + - - +
713u ALA* 4.1 6.1 - - - +
714u GLU 3.4 0.6 - - - -
715u ALA* 1.3 79.6 - - - +
717u THR* 1.3 71.1 + - - +
718u PRO 3.9 0.7 - - - -
719u TYR* 3.2 32.9 + - + +
756u LEU* 6.2 1.8 - - + -
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Residues in contact with THR 717 (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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713u ALA 3.8 7.9 + - - -
714u GLU* 3.9 16.6 - - - -
715u ALA 4.4 2.0 - - - -
716u ALA* 1.3 82.2 - - - +
718u PRO* 1.3 54.9 - - - +
719u TYR* 5.3 0.4 - - - -
756u LEU* 6.0 0.4 - - - +
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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
------------------------------------------------------------
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