Contacts of the helix formed by residues 994 - 1001 (chain A) in PDB entry 2G56
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 ASN 994 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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779A TYR* 5.9 0.4 - - - -
992A ILE* 3.6 4.2 - - - +
993A GLN* 1.3 82.6 + - + +
995A MET* 1.3 63.8 + - - +
996A THR* 2.8 22.5 + - - -
997A GLU* 2.8 57.9 + - + +
998A PHE* 3.0 22.3 + - - +
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Residues in contact with MET 995 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A TYR* 3.6 20.0 - - + +
688A LEU* 3.8 29.4 - - + +
689A LEU* 3.3 38.8 - - + -
696A THR* 5.3 6.1 - - - -
779A TYR* 3.5 43.1 - - + +
992A ILE* 4.3 0.4 - - - +
994A ASN* 1.3 72.6 + - - +
996A THR* 1.3 63.8 + - - +
998A PHE* 3.3 7.9 + - - +
999A LYS* 3.0 38.3 + - - +
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Residues in contact with THR 996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994A ASN* 2.8 18.7 + - - -
995A MET* 1.3 74.0 - - - +
997A GLU* 1.3 63.1 + - - -
999A LYS* 3.2 8.8 + - - +
1000A ARG* 3.0 42.2 + - + +
760B PRO* 4.8 6.2 - - - +
761B SER* 3.9 37.3 + - - +
763B LEU 5.9 2.2 - - - +
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Residues in contact with GLU 997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993A GLN* 6.0 0.7 - - - +
994A ASN* 2.8 41.9 + - + +
996A THR* 1.3 72.7 - - - +
998A PHE* 1.3 64.0 + - - +
1000A ARG* 3.3 16.1 + - - +
1001A GLY* 3.0 21.3 + - - -
1009B LYS* 4.4 13.5 + - - +
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Residues in contact with PHE 998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A LEU* 3.7 36.6 - - + -
690A MET* 3.8 15.0 - - + -
769A VAL* 4.5 3.1 - - + -
771A LEU* 4.0 13.9 - - + -
777A PHE* 3.4 37.2 - + + -
954A VAL* 5.4 0.9 - - + -
990A GLU* 5.5 1.8 - - - -
992A ILE* 3.5 37.2 - - + -
994A ASN 3.0 13.6 + - - +
995A MET 3.4 7.9 - - - +
996A THR 3.2 0.2 - - - -
997A GLU* 1.3 79.5 - - - +
999A LYS* 1.3 66.6 + - + +
1001A GLY* 3.3 7.6 + - - -
1002A LEU* 3.6 43.1 + - + +
1009B LYS* 6.0 0.4 - - - +
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Residues in contact with LYS 999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688A LEU 2.8 27.8 + - - -
689A LEU* 3.8 16.8 - - - +
691A THR 2.5 30.2 + - - +
692A GLU* 3.5 17.2 + - - +
694A ALA* 4.0 18.6 + - - +
769A VAL* 4.2 14.1 - - + +
995A MET* 3.0 23.6 + - - +
996A THR* 3.8 5.6 - - - +
998A PHE* 1.3 80.1 - - + +
1000A ARG* 1.3 64.8 + - + +
1002A LEU* 3.1 15.9 + - - +
1004A LEU* 5.0 2.6 - - + +
767B ARG* 3.0 19.7 + - - +
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Residues in contact with ARG1000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996A THR* 3.0 37.2 + - + +
997A GLU* 3.6 13.2 - - - +
999A LYS* 1.3 79.0 - - + +
1001A GLY* 1.3 57.0 + - - +
1002A LEU 3.2 3.8 + - - -
763B LEU 5.5 6.3 - - - -
765B ARG* 6.0 2.4 - - - +
767B ARG* 3.8 7.9 + - - +
914B GLN* 4.4 22.4 + - - +
1006B PRO* 3.4 2.3 - - - +
1007B LEU* 2.8 61.0 + - + +
1008B VAL 3.1 26.7 + - - -
1009B LYS* 4.7 0.4 - - - +
1010B PRO* 3.8 23.9 - - - +
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Residues in contact with GLY1001 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997A GLU 3.0 15.4 + - - -
998A PHE 3.3 2.0 + - - -
999A LYS 3.2 0.6 - - - -
1000A ARG* 1.3 75.1 - - - +
1002A LEU* 1.3 70.2 + - - +
1003A PRO* 4.6 0.3 - - - +
1006B PRO* 3.5 13.0 - - - +
1007B LEU 4.4 6.7 - - - -
1009B LYS* 4.1 25.9 - - - -
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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