Contacts of the helix formed by residues 591 - 607 (chain q) 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 ASP 591 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589q GLU* 3.5 5.7 - - - +
590q ALA* 1.3 77.8 - - + +
592q TYR* 1.3 63.8 + - - +
593q LEU 3.5 2.0 + - - +
594q GLU* 4.0 10.6 + - + +
595q ALA* 3.9 13.9 + - - +
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Residues in contact with TYR 592 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589q GLU* 4.9 10.1 - - + +
590q ALA 3.7 4.0 + - - +
591q ASP* 1.3 72.1 - - - +
593q LEU* 1.3 60.7 + - - +
595q ALA* 3.1 8.6 + - - +
596q CYS* 2.8 28.7 + - - +
693q PRO* 4.1 29.1 - - + +
738q LEU* 4.8 9.2 - - + +
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Residues in contact with LEU 593 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591q ASP* 3.5 1.6 - - - +
592q TYR* 1.3 75.1 - - - +
594q GLU* 1.3 65.3 + - - +
596q CYS* 3.0 10.3 + - - +
597q VAL* 2.9 21.2 + - - +
621q GLU* 6.5 0.7 - - + -
625q ALA* 6.4 1.8 - - + -
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Residues in contact with GLU 594 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591q ASP* 4.0 12.1 + - + +
592q TYR 3.3 0.4 - - - -
593q LEU* 1.3 77.1 - - - +
595q ALA* 1.3 65.1 + - - +
597q VAL* 3.0 9.7 + - - +
598q VAL* 3.0 22.4 + - - +
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Residues in contact with ALA 595 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589q GLU* 5.1 11.4 - - + -
591q ASP 3.9 7.7 + - - +
592q TYR* 3.1 15.3 + - + +
594q GLU* 1.3 78.9 - - - +
596q CYS* 1.3 63.1 + - - +
598q VAL* 3.2 7.4 + - - +
599q SER* 3.0 22.9 + - - -
738q LEU* 5.5 9.0 - - + -
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Residues in contact with CYS 596 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592q TYR 2.8 13.1 + - - +
593q LEU* 3.3 11.9 - - - +
595q ALA* 1.3 77.6 - - - +
597q VAL* 1.3 62.1 + - - +
599q SER* 3.3 7.6 + - - -
600q VAL* 3.1 21.8 + - - +
614q VAL* 5.9 5.8 - - + -
615q PHE 6.2 0.4 - - - +
691q LEU* 5.4 10.5 - - + -
693q PRO* 5.3 11.9 - - + -
738q LEU* 6.2 2.2 - - + +
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Residues in contact with VAL 597 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593q LEU 2.9 11.5 + - - +
594q GLU* 3.4 11.0 - - - +
596q CYS* 1.3 78.8 - - - +
598q VAL* 1.3 62.4 - - - +
600q VAL* 3.2 7.7 + - - +
601q LEU* 3.2 21.1 + - - +
625q ALA* 6.5 0.7 - - + -
628q MET* 5.6 11.0 - - + -
629q LEU* 5.9 8.3 - - + +
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Residues in contact with VAL 598 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594q GLU 3.0 11.5 + - - +
595q ALA* 3.7 9.9 - - - +
597q VAL* 1.3 78.0 - - - +
599q SER* 1.3 62.3 + - - +
601q LEU* 3.2 8.8 + - - +
602q GLN* 3.0 22.2 + - - +
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Residues in contact with SER 599 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595q ALA 3.0 12.7 + - - -
596q CYS* 3.7 8.7 - - - -
598q VAL* 1.3 73.6 - - - +
600q VAL* 1.3 66.8 + - - +
602q GLN* 3.2 7.4 + - - +
603q ILE* 3.0 23.6 + - - +
691q LEU* 5.2 8.5 - - - -
736q PHE* 5.0 16.8 - - - -
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Residues in contact with VAL 600 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596q CYS 3.1 12.6 + - - +
597q VAL* 3.6 10.1 - - - +
598q VAL 3.2 0.2 - - - -
599q SER* 1.3 77.6 - - - +
601q LEU* 1.3 63.2 + - - +
603q ILE* 3.2 7.5 + - - +
604q HIS* 3.0 22.9 + - - +
612q ILE* 5.7 6.5 - - + -
629q LEU* 5.9 7.0 - - + -
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Residues in contact with LEU 601 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597q VAL 3.2 9.6 + - - +
598q VAL* 3.7 9.0 - - - +
600q VAL* 1.3 76.4 - - - +
602q GLN* 1.3 67.0 + - - +
604q HIS* 3.2 7.5 + - - +
605q VAL* 3.1 21.8 + - - +
632q ARG* 5.5 11.4 - - + -
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Residues in contact with GLN 602 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598q VAL 3.0 13.3 + - - +
599q SER* 3.7 10.5 - - - +
600q VAL 3.2 0.2 - - - -
601q LEU* 1.3 75.6 - - - +
603q ILE* 1.3 66.4 + - - +
605q VAL* 3.1 5.2 + - - +
606q THR* 3.0 28.7 + - - -
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Residues in contact with ILE 603 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599q SER 3.0 13.8 + - - +
600q VAL* 3.5 10.8 - - - +
602q GLN* 1.3 77.7 - - - +
604q HIS* 1.3 57.7 - - - +
606q THR* 5.2 0.7 - - - -
607q GLN* 2.8 44.8 + - + +
689q TYR* 5.2 14.6 - - + -
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Residues in contact with HIS 604 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600q VAL 3.0 12.9 + - - +
601q LEU* 3.7 9.6 - - - +
602q GLN 3.2 0.4 - - - -
603q ILE* 1.3 78.4 - - - +
605q VAL* 1.3 64.7 + - - +
607q GLN 4.3 6.6 - - - +
640q ILE* 5.4 3.4 - - - +
643q LEU* 5.3 11.9 - - + -
667q GLY 5.3 4.9 - - - +
669q ARG* 5.1 16.6 - - + -
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Residues in contact with VAL 605 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601q LEU 3.1 15.3 + - - +
602q GLN* 3.9 4.3 - - - +
604q HIS* 1.3 81.4 - - - +
606q THR* 1.3 62.9 + - - +
607q GLN 4.5 1.6 - - - +
640q ILE* 5.1 15.0 - - + -
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Residues in contact with THR 606 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602q GLN* 3.0 15.1 + - - -
603q ILE* 5.2 0.7 - - - -
605q VAL* 1.3 80.1 - - - +
607q GLN* 1.3 67.1 + - - +
608q PRO 3.8 0.7 - - - -
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Residues in contact with GLN 607 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603q ILE* 2.8 33.1 + - + +
604q HIS* 4.3 7.1 - - - +
605q VAL 4.5 1.2 - - - +
606q THR* 1.3 79.2 - - - +
608q PRO* 1.3 73.2 - - - +
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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
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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