Contacts of the helix formed by residues 938 - 946 (chain D) in PDB entry 6GHM
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 GLU 938 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LYS* 3.4 24.2 - - + +
261A ARG* 2.4 46.6 + - - -
933D SER* 3.0 12.2 + - - -
936D GLU* 4.0 21.3 - - + +
937D GLY* 1.3 74.1 - - - +
939D PHE* 1.3 65.0 + - - +
940D ASP* 3.2 14.5 - - - +
941D LEU* 3.2 10.5 + - + +
942D VAL* 3.1 25.6 + - - +
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Residues in contact with PHE 939 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041C THR* 4.0 20.4 - - + +
937D GLY 3.0 5.7 + - - -
938D GLU* 1.3 74.9 - - - +
940D ASP* 1.3 63.1 + - - +
942D VAL* 3.1 7.2 + - + +
943D GLN* 3.1 55.7 + - + +
973D GLU* 3.3 43.1 - - + -
974D ILE* 3.7 29.6 - - + -
977D PHE* 3.5 39.7 - + + -
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Residues in contact with ASP 940 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938D GLU* 3.4 19.1 - - - +
939D PHE* 1.3 76.0 - - - +
941D LEU* 1.3 70.6 + - - +
943D GLN* 3.5 14.9 + - - +
944D ARG* 3.5 17.7 + - - +
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Residues in contact with LEU 941 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ARG* 3.4 32.5 - - - +
929D LEU* 4.0 22.2 - - + -
933D SER* 3.7 20.9 - - - +
938D GLU* 3.2 12.3 + - - +
940D ASP* 1.3 85.4 + - - +
942D VAL* 1.3 63.1 + - - +
944D ARG* 3.1 8.4 + - + -
945D ILE* 2.8 46.8 + - + +
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Residues in contact with VAL 942 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930D LEU* 4.0 14.8 - - + -
933D SER* 3.3 33.2 - - - +
934D SER* 3.8 10.3 - - - +
938D GLU 3.1 17.3 + - - +
939D PHE* 3.1 11.4 + - + +
941D LEU* 1.3 75.7 - - - +
943D GLN* 1.3 62.2 + - - +
945D ILE* 4.0 3.8 - - - +
946D ILE* 3.2 25.6 + - - +
974D ILE* 4.1 16.2 - - + -
977D PHE* 4.0 22.2 - - + -
978D LEU* 4.1 10.3 - - + -
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Residues in contact with GLN 943 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939D PHE* 3.1 58.0 + - + +
940D ASP* 3.8 13.7 - - - +
941D LEU 3.2 0.4 - - - -
942D VAL* 1.3 76.3 - - - +
944D ARG* 1.3 56.2 + - - +
946D ILE* 3.6 1.6 - - - +
947D TYR* 3.2 31.0 - - - -
977D PHE* 4.0 23.4 - - + -
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Residues in contact with ARG 944 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940D ASP 3.5 8.8 + - - +
941D LEU* 3.1 14.4 + - + +
943D GLN* 1.3 79.6 - - - +
945D ILE* 1.3 65.2 + - + +
946D ILE 3.1 1.4 + - - -
947D TYR* 3.3 19.7 + - - +
948D GLU* 4.1 7.0 - - - +
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Residues in contact with ILE 945 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926D PRO* 3.7 29.2 - - + +
929D LEU* 3.7 28.5 - - + -
930D LEU* 4.0 32.1 - - + +
933D SER* 4.4 1.3 - - - +
941D LEU* 2.8 34.7 + - + +
942D VAL* 4.0 6.3 - - - +
944D ARG* 1.3 73.0 - - - +
946D ILE* 1.3 64.9 + - - +
947D TYR 3.2 0.4 - - - -
948D GLU* 3.0 37.2 + - - +
949D VAL* 3.4 10.0 + - - +
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Residues in contact with ILE 946 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930D LEU* 4.5 7.6 - - + -
942D VAL 3.2 20.0 + - - +
943D GLN 3.6 13.2 - - - +
945D ILE* 1.3 80.9 - - - +
947D TYR* 1.3 72.7 + - + +
948D GLU 3.1 0.2 - - - -
949D VAL* 3.1 29.7 + - + +
952D PRO* 3.9 23.0 - - + +
977D PHE* 4.1 10.8 - - + -
978D LEU* 3.7 29.6 - - + -
981D PHE* 3.6 45.2 - - + -
983D VAL* 4.8 0.2 - - + -
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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