Contacts of the helix formed by residues 721 - 736 (chain M) 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 LYS 721 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708M LYS 6.1 0.4 - - - +
711M GLU* 5.8 5.2 - - + -
712M VAL* 5.9 4.0 - - + +
716M ASN* 4.1 11.0 - - + -
717M GLU 3.1 26.0 - - - +
718M ASP 4.1 1.6 - - - +
719M THR 2.9 5.5 + - - +
720M ILE* 1.3 78.7 - - - +
722M GLU* 1.3 57.9 + - - +
723M MET 3.3 0.9 - - - -
724M LEU* 3.7 8.7 - - + +
725M ARG* 2.9 32.5 + - + +
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Residues in contact with GLU 722 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718M ASP 4.1 9.8 + - - +
720M ILE 3.4 3.2 - - - +
721M LYS* 1.3 78.9 - - - +
723M MET* 1.3 51.6 + - - +
725M ARG* 5.1 1.8 - - - -
726M ILE* 2.7 41.3 + - + +
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Residues in contact with MET 723 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399 SER* 6.2 2.7 - - - -
720M ILE* 4.2 9.4 + - - +
721M LYS 3.3 0.4 - - - -
722M GLU* 1.3 77.2 - - - +
724M LEU* 1.3 55.3 + - - +
726M ILE* 4.6 1.8 - - - -
727M ARG* 2.5 41.8 + - + +
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Residues in contact with LEU 724 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708M LYS* 6.1 5.2 - - + -
711M GLU* 5.1 14.4 - - + -
720M ILE 3.9 12.4 + - - +
721M LYS* 3.3 12.1 + - + +
722M GLU 3.3 0.4 - - - -
723M MET* 1.3 76.6 - - - +
725M ARG* 1.3 61.5 + - - +
727M ARG* 3.9 1.5 - - - +
728M ARG* 2.9 30.8 + - - +
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Residues in contact with ARG 725 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708M LYS* 5.6 11.2 - - + +
721M LYS* 2.9 17.0 + - + +
722M GLU* 4.6 1.8 - - - +
724M LEU* 1.3 73.8 - - - +
726M ILE* 1.3 61.4 + - - +
728M ARG* 3.9 3.8 - - - +
729M SER* 2.9 32.1 + - - -
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Residues in contact with ILE 726 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359 ASP 2.6 9.0 - - - +
389 ASN* 2.1 46.6 - - + +
399 SER* 4.3 9.4 - - - +
722M GLU* 2.7 23.2 + - + +
723M MET* 4.6 2.0 - - - -
725M ARG* 1.3 78.3 - - - +
727M ARG* 1.3 51.6 + - - +
729M SER* 4.7 1.3 - - - -
730M VAL 2.9 4.9 + - - -
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Residues in contact with ARG 727 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359 ASP* 0.3 183.1 - - + +
369 GLN 4.8 0.4 - - - +
399 SER* 4.9 8.5 - - - -
723M MET* 2.5 27.4 + - + +
724M LEU* 4.2 1.6 - - - +
726M ILE* 1.3 73.7 - - - +
728M ARG* 1.3 43.0 - - - +
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Residues in contact with ARG 728 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329 THR* 5.6 0.2 - - - -
339 LEU 2.7 16.5 - - - +
359 ASP* 2.9 7.8 + - - -
704M TRP* 5.1 16.6 - - + +
724M LEU 2.9 21.5 + - - +
725M ARG* 3.9 4.9 - - - +
727M ARG* 1.3 76.5 - - - +
729M SER* 1.3 51.7 + - - +
731M GLN* 3.7 4.4 - - - +
732M ALA* 2.9 13.3 + - - +
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Residues in contact with SER 729 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329 THR* 3.6 25.1 - - - -
339 LEU* 1.3 65.9 - - - +
349 ARG 2.2 1.2 + - - -
389 ASN* 4.2 5.8 - - - -
725M ARG 2.9 18.3 + - - -
726M ILE* 4.3 2.2 - - - -
728M ARG* 1.3 67.3 - - - +
730M VAL* 1.3 49.9 + - - +
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Residues in contact with VAL 730 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339 LEU* 4.2 0.7 - - - -
349 ARG* 0.7 145.1 + - - +
359 ASP* 1.6 57.7 - - - +
369 GLN 2.9 0.2 - - - -
379 ILE* 2.4 22.4 + - - +
389 ASN* 1.9 36.9 - - - +
726M ILE 2.9 4.2 + - - -
729M SER* 1.3 65.2 - - - +
731M GLN* 1.3 8.3 - - - -
734M TYR* 2.9 4.7 + - - +
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Residues in contact with GLN 731 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349 ARG* 0.9 71.4 - - - +
359 ASP* 0.7 63.3 - - + +
369 GLN* 3.5 7.4 - - + +
692M SER* 4.9 17.7 - - - -
727M ARG 3.2 9.2 - - - +
728M ARG* 3.7 5.2 - - - +
730M VAL 1.3 5.0 - - - -
732M ALA* 1.3 53.9 + - - +
734M TYR* 3.8 1.0 - - - +
735M ASN* 2.9 19.1 + - - +
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Residues in contact with ALA 732 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329 THR* 1.9 36.3 - - - +
339 LEU* 2.6 9.3 + - - +
349 ARG* 1.7 14.0 - - - +
697M PRO* 6.5 1.3 - - - -
728M ARG 2.9 9.6 + - - +
731M GLN* 1.3 66.8 - - - +
733M THR* 1.3 55.2 + - - -
735M ASN* 3.3 6.6 + - - +
736M THR* 2.9 28.1 + - - -
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Residues in contact with THR 733 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339 LEU* 1.6 48.5 - - - +
349 ARG 1.3 49.7 - - - +
379 ILE* 4.0 13.7 - - - -
439 THR 5.3 5.9 - - - +
732M ALA 1.3 52.9 - - - -
734M TYR* 1.3 59.2 + - - +
736M THR* 3.3 18.3 + - - -
737M GLN 3.6 11.4 + - - +
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Residues in contact with TYR 734 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349 ARG* 2.3 38.9 - - + +
369 GLN* 4.6 8.3 - - + -
379 ILE* 4.3 10.9 - - + +
730M VAL 2.9 5.8 + - - +
731M GLN* 3.8 0.9 - - - +
733M THR* 1.3 68.6 - - - +
735M ASN* 1.3 58.5 + - - +
737M GLN* 3.4 12.4 + - - +
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Residues in contact with ASN 735 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697M PRO* 5.0 17.4 - - + +
731M GLN 2.9 18.5 + - - +
732M ALA* 3.8 7.2 - - - +
733M THR 3.3 0.2 - - - -
734M TYR* 1.3 74.6 - - - +
736M THR* 1.3 59.9 + - - +
737M GLN* 3.1 6.2 + - - +
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Residues in contact with THR 736 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732M ALA 2.9 16.4 + - - -
733M THR* 3.6 11.7 - - - -
734M TYR 3.2 0.8 - - - -
735M ASN* 1.3 75.1 - - - +
737M GLN* 1.3 71.8 + - - +
738M VAL 3.3 9.5 + - - -
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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
------------------------------------------------------------
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