Contacts of the helix formed by residues 720 - 731 (chain M) in PDB entry 6G0L
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 MET 720 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-20I C 4.0 5.6 - - - -
657M LYS* 3.7 44.9 - - + +
660M ASN* 4.2 13.5 - - - +
664M LEU* 5.6 6.7 - - + -
718M SER* 4.3 8.1 - - - -
719M GLN* 1.3 98.3 - - - +
721M VAL* 1.3 63.3 + - - +
722M ARG* 3.3 5.3 + - + +
723M MET* 3.7 34.5 + - + +
724M LEU* 3.6 17.2 + - - +
789M PHE* 5.5 2.9 - - + -
790M ASP* 3.9 23.6 - - - +
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Residues in contact with VAL 721 (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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-20I C 3.3 43.9 + - - +
-19I G 4.0 22.0 - - - +
719M GLN 4.3 3.8 - - - +
720M MET* 1.3 72.7 - - - +
722M ARG* 1.3 79.5 + - + +
723M MET 3.4 0.2 - - - -
724M LEU* 3.6 23.1 + - + +
725M ASP* 3.5 17.3 + - - +
740M ARG* 4.1 5.6 + - - +
742M ASP* 5.3 5.2 - - + +
770M SER* 5.5 1.6 - - - +
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Residues in contact with ARG 722 (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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657M LYS* 5.7 6.7 - - - +
664M LEU* 4.5 19.2 + - + -
720M MET* 3.3 3.0 - - + +
721M VAL* 1.3 92.4 - - + +
723M MET* 1.3 59.8 + - - +
724M LEU 3.2 0.4 - - - -
725M ASP* 3.0 19.3 + - - +
726M ILE* 2.9 33.6 + - + +
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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
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661M HIS* 3.8 49.4 - - + +
664M LEU* 5.3 4.3 - - + +
696M LYS* 6.4 0.9 - - + -
697M MET* 3.9 22.2 - - - -
718M SER* 4.7 4.0 - - - +
720M MET* 3.7 30.6 + - + +
721M VAL 3.4 0.4 - - - -
722M ARG* 1.3 77.2 - - - +
724M LEU* 1.3 57.9 + - - +
726M ILE* 3.5 11.7 - - + +
727M LEU* 2.9 35.5 + - + +
789M PHE* 3.8 38.6 - - + -
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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
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716M ILE 5.0 2.5 - - - +
718M SER* 3.8 27.4 - - - +
719M GLN 5.8 0.2 - - - +
720M MET 3.6 14.6 - - - +
721M VAL* 3.6 11.2 + - + +
722M ARG 3.2 0.6 - - - -
723M MET* 1.3 78.3 - - - +
725M ASP* 1.3 56.6 + - - +
727M LEU* 3.5 10.5 + - + +
728M GLY* 2.9 22.5 + - - -
740M ARG* 3.4 37.6 + - + +
741M LEU 5.0 1.8 - - - +
742M ASP* 4.4 6.5 - - + -
768M LEU* 4.0 21.6 - - + +
769M LEU 3.3 27.6 - - - +
770M SER* 3.4 15.0 - - - +
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Residues in contact with ASP 725 (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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721M VAL 3.5 13.6 + - - +
722M ARG* 3.0 21.8 + - - +
724M LEU* 1.3 75.5 - - - +
726M ILE* 1.3 59.8 + - + +
728M GLY* 3.0 3.8 + - - +
729M ASP* 2.9 39.8 + - - +
740M ARG* 3.3 28.5 + - - +
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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
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661M HIS* 3.4 36.6 - - + +
663M TYR* 3.3 30.7 - - + +
664M LEU* 4.8 3.4 - - + -
690M LEU* 4.4 18.6 - - + +
697M MET* 5.9 2.5 - - + -
722M ARG* 2.9 23.2 + - + +
723M MET* 3.2 19.7 + - + +
725M ASP* 1.3 77.7 - - + +
727M LEU* 1.3 59.8 + - + +
729M ASP* 3.1 10.0 + - + +
730M TYR* 2.9 27.6 + - + +
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Residues in contact with LEU 727 (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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697M MET* 4.0 28.0 - - + -
700M LEU* 4.7 6.7 - - + -
716M ILE* 3.8 17.3 - - + -
718M SER* 4.7 2.7 - - - +
723M MET* 2.9 34.4 + - + +
724M LEU* 3.8 8.1 - - + +
726M ILE* 1.3 77.4 - - + +
728M GLY* 1.3 57.4 + - - +
730M TYR* 4.3 7.4 - - + +
731M LEU* 2.9 44.6 + - + +
738M PHE* 4.7 0.4 - - - -
768M LEU* 4.2 19.5 - - + -
789M PHE* 3.6 32.1 - - + -
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Residues in contact with GLY 728 (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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724M LEU 2.9 16.4 + - - -
725M ASP* 3.0 7.2 + - - -
727M LEU* 1.3 78.0 - - - +
729M ASP* 1.3 60.4 + - - +
732M SER* 3.0 25.2 + - - -
738M PHE* 3.5 23.9 - - - -
740M ARG* 5.1 4.7 - - - -
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Residues in contact with ASP 729 (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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690M LEU* 5.4 5.9 - - + +
725M ASP* 2.9 23.1 + - - +
726M ILE* 3.1 9.5 + - + +
728M GLY* 1.3 79.8 - - - +
730M TYR* 1.3 58.4 + - - +
732M SER* 3.4 5.5 + - - -
733M ILE* 3.3 31.2 - - - +
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Residues in contact with TYR 730 (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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687M LEU* 3.6 40.8 - - + +
690M LEU* 4.0 24.4 - - + +
691M ILE* 3.3 37.1 - - + +
697M MET* 3.8 29.2 - - + -
700M LEU* 6.2 2.5 - - + -
701M ASP* 3.5 23.2 + - + +
704M LEU* 6.1 1.3 - - + -
726M ILE* 2.9 15.4 + - + +
727M LEU* 3.4 7.2 + - + +
729M ASP* 1.3 75.2 - - - +
731M LEU* 1.3 85.3 + - + +
732M SER 3.3 1.7 + - - -
733M ILE* 3.5 8.4 + - - -
734M LYS* 3.6 25.2 + - + +
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Residues in contact with LEU 731 (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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700M LEU* 6.2 3.4 - - + -
704M LEU* 4.5 10.3 - - + -
716M ILE* 5.4 3.1 - - + -
727M LEU* 2.9 35.4 + - + +
730M TYR* 1.3 98.0 - - + +
732M SER* 1.3 61.7 + - - +
733M ILE 3.3 0.2 - - - -
734M LYS* 3.7 4.9 + - + +
736M ILE* 3.1 54.7 + - + +
738M PHE* 3.9 20.2 - - + -
766M VAL* 3.9 30.3 - - + -
768M LEU* 4.6 8.5 - - + -
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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
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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