Contacts of the helix formed by residues 716 - 726 (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 SER 716 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715q CYS* 1.3 78.1 - - - +
717q LYS* 1.3 66.7 + - - +
718q ALA* 3.1 4.9 - - - -
719q SER* 3.2 12.4 + - - -
720q ALA* 3.0 21.5 + - - +
748q LEU* 4.2 1.1 - - - -
749q GLU* 3.3 17.7 - - - +
750q GLU 3.6 11.0 - - - -
751q THR* 4.0 12.8 - - - -
752q THR* 4.0 14.1 - - - -
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Residues in contact with LYS 717 (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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716q SER* 1.3 71.6 - - - +
718q ALA* 1.3 58.7 + - - +
720q ALA* 3.0 9.5 + - - +
721q ASN* 2.9 29.0 + - - +
744q TYR 4.8 8.1 - - - +
748q LEU* 3.7 17.9 - - + +
749q GLU 2.8 17.6 + - - +
750q GLU* 4.1 9.0 - - - +
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Residues in contact with ALA 718 (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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716q SER* 3.1 3.8 - - - -
717q LYS* 1.3 80.1 - - - +
719q SER* 1.3 63.3 + - - +
721q ASN* 3.1 8.8 + - - +
722q GLN* 3.0 20.1 + - - +
750q GLU 3.3 15.7 + - - +
751q THR* 5.0 6.7 - - - -
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Residues in contact with SER 719 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679q GLU* 5.4 8.7 - - - +
715q CYS* 4.7 8.3 - - - -
716q SER* 3.2 21.3 + - - -
718q ALA* 1.3 79.8 - - - +
720q ALA* 1.3 62.9 + - - +
722q GLN* 3.0 8.5 + - - +
723q ARG* 2.9 23.9 + - - +
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Residues in contact with ALA 720 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715q CYS* 5.1 5.1 - - + +
716q SER 3.0 12.7 + - - +
717q LYS* 3.0 13.6 + - - +
719q SER* 1.3 77.5 - - - +
721q ASN* 1.3 63.0 + - - +
723q ARG* 3.4 6.1 + - - +
724q ALA* 3.1 22.1 + - - +
744q TYR* 6.4 2.0 - - + -
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Residues in contact with ASN 721 (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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717q LYS 2.9 11.7 + - - +
718q ALA* 3.1 10.3 + - - +
720q ALA* 1.3 78.7 - - - +
722q GLN* 1.3 61.9 + - - +
724q ALA* 3.2 7.1 + - - +
725q GLY* 3.0 20.3 + - - -
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Residues in contact with GLN 722 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679q GLU* 4.3 30.7 - - + +
680q THR* 5.7 4.0 - - - -
718q ALA 3.0 11.9 + - - +
719q SER* 3.0 13.0 + - - +
721q ASN* 1.3 77.6 - - - +
723q ARG* 1.3 62.0 + - - +
725q GLY* 3.1 11.5 + - - +
726q ARG* 3.3 8.8 + - - +
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Residues in contact with ARG 723 (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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679q GLU* 5.3 10.3 - - + +
690q VAL* 3.9 15.0 - - + +
692q ASP* 4.8 18.4 - - + -
719q SER 2.9 15.2 + - - +
720q ALA* 3.7 7.0 - - - +
721q ASN 3.2 0.2 - - - -
722q GLN* 1.3 77.8 - - - +
724q ALA* 1.3 62.4 + - - +
726q ARG* 3.2 20.6 + - - +
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Residues in contact with ALA 724 (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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580q VAL* 4.2 12.4 - - + +
690q VAL* 4.9 0.2 - - - -
720q ALA 3.1 11.2 + - - +
721q ASN* 3.2 10.1 + - - +
723q ARG* 1.3 78.4 - - - +
725q GLY* 1.3 63.3 + - - +
727q ALA* 3.0 24.8 + - - +
728q GLY 4.1 0.9 + - - -
735q CYS* 4.0 25.3 - - + +
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Residues in contact with GLY 725 (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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577q ARG* 5.0 11.1 - - - +
580q VAL* 5.8 1.3 - - - -
721q ASN 3.0 13.5 + - - -
722q GLN* 3.1 7.0 + - - -
724q ALA* 1.3 77.3 - - - +
726q ARG* 1.3 62.3 + - - +
728q GLY* 2.9 18.8 + - - -
729q ARG* 3.9 3.5 + - - +
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Residues in contact with ARG 726 (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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613q LEU* 5.6 9.6 - - + -
678q ALA 4.9 12.6 - - - +
679q GLU 5.3 2.7 - - - +
687q ILE* 3.8 18.9 - - + +
690q VAL* 5.5 3.1 - - + -
722q GLN 3.3 7.5 + - - +
723q ARG* 3.2 15.5 + - - +
724q ALA 3.1 0.8 - - - -
725q GLY* 1.3 76.2 - - - +
727q ALA* 1.3 60.8 - - - +
728q GLY 3.4 0.5 + - - -
729q ARG* 3.8 13.2 + - - +
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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