Contacts of the helix formed by residues 74 - 82 (chain R) in PDB entry 6GYK
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 PRO 74 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72R ARG 4.3 0.2 - - - +
73R LEU* 1.3 98.3 - - + +
75R MET* 1.3 62.1 + - + +
76R PHE* 3.4 29.6 + - + -
77R LEU* 3.6 8.1 + - + -
78R ALA* 2.9 30.2 + - - +
120R TYR* 5.3 6.1 - - + -
224R VAL* 4.1 26.5 - - + +
226R PRO* 5.8 7.0 - - + -
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Residues in contact with MET 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B THR* 4.7 17.3 - - + +
559B SER* 6.4 1.1 - - - -
560B GLU* 4.1 33.4 - - + +
372Q SER* 5.8 5.6 - - - -
73R LEU 4.8 2.0 - - - +
74R PRO* 1.3 76.0 - - + +
76R PHE* 1.3 59.3 + - + +
78R ALA* 4.3 4.7 - - - -
79R GLU* 2.9 39.0 + - + +
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Residues in contact with PHE 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R PRO* 3.9 26.7 - - + -
75R MET* 1.3 78.8 - - + +
77R LEU* 1.3 80.8 + - + +
79R GLU* 3.9 3.6 - - - +
80R LYS* 2.9 28.4 + - + +
118R HIS* 6.0 2.9 - + - -
120R TYR* 3.9 25.1 - + - -
226R PRO* 6.4 1.6 - - + -
237R VAL* 5.4 14.8 - - + -
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Residues in contact with LEU 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73R LEU* 3.6 20.6 - - + -
74R PRO* 3.6 11.3 + - + +
75R MET 3.4 0.2 - - - -
76R PHE* 1.3 95.5 - - + +
78R ALA* 1.3 61.0 + - - +
80R LYS* 3.3 18.5 + - + +
81R TRP* 2.9 77.7 + - + +
106R LEU* 5.2 2.0 - - + -
108R LEU* 3.7 29.6 - - + -
120R TYR* 4.3 17.9 - - + +
224R VAL* 5.5 0.7 - - + -
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Residues in contact with ALA 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372Q SER* 3.6 27.6 - - - +
374Q VAL* 5.3 4.0 - - + -
73R LEU* 3.4 14.5 - - + +
74R PRO 2.9 20.2 + - - +
75R MET* 3.9 4.7 - - - +
77R LEU* 1.3 74.7 - - - +
79R GLU* 1.3 60.7 - - + +
81R TRP* 2.9 19.8 + - - +
82R ARG* 3.0 25.5 + - - +
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Residues in contact with GLU 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371Q ASP 5.7 0.5 - - - +
75R MET* 2.9 25.9 + - + +
76R PHE* 4.1 4.3 - - - +
78R ALA* 1.3 77.9 - - + +
80R LYS* 1.3 61.7 + - - +
82R ARG* 3.3 34.2 + - - +
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Residues in contact with LYS 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76R PHE* 2.9 20.5 + - + +
77R LEU* 3.4 24.5 - - + +
78R ALA 3.1 0.2 - - - -
79R GLU* 1.3 78.1 - - - +
81R TRP* 1.3 63.6 + - + +
82R ARG 3.5 2.6 + - - -
117R PRO* 6.3 3.8 - - - -
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Residues in contact with TRP 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q LEU* 5.2 0.7 - - + -
374Q VAL* 3.9 25.4 - - + -
386Q MET* 3.3 39.3 - - + -
388Q PRO* 5.3 8.5 - - - +
71R VAL* 5.5 1.3 - - + -
73R LEU* 3.3 38.6 - - + -
77R LEU* 2.9 46.5 + - + +
78R ALA* 2.9 8.7 + - - +
80R LYS* 1.3 84.1 - - + +
82R ARG* 1.3 66.7 + - - +
92R LEU* 6.1 3.6 - - - +
93R GLY 6.2 0.2 - - - -
106R LEU* 4.5 10.5 - - + -
108R LEU* 4.2 19.8 - - + +
224R VAL* 6.0 0.4 - - + -
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Residues in contact with ARG 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Q LYS* 5.2 11.6 + - - -
370Q SER* 5.1 3.2 + - - -
371Q ASP 3.4 24.0 + - - -
372Q SER* 4.4 2.0 - - - +
373Q TYR 4.3 15.9 + - - +
374Q VAL* 6.0 2.8 - - - +
388Q PRO* 3.2 33.6 - - - +
389Q ALA 3.9 17.6 + - - -
390Q ASP* 5.8 0.2 - - - +
78R ALA* 3.0 25.7 + - - +
79R GLU* 3.5 36.4 + - - +
80R LYS 3.3 5.0 - - - -
81R TRP* 1.3 82.2 - - - +
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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