Contacts of the helix formed by residues 984 - 991 (chain A) in PDB entry 2XTA
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 ALA 984 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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952A GLU* 3.6 26.9 - - + +
953A PHE* 3.9 9.9 - - - +
956A VAL* 3.7 25.4 - - + -
981A VAL 2.7 15.0 + - - +
983A GLY* 1.4 77.0 - - - +
985A GLN* 1.3 63.6 + - - +
986A SER* 3.3 3.6 - - - -
987A ILE* 3.1 14.4 + - + +
988A ILE* 3.1 15.4 + - + +
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Residues in contact with GLN 985 (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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981A VAL* 3.6 1.3 + - - +
982A ASN* 3.2 25.9 + - + +
983A GLY 3.5 1.2 - - - -
984A ALA* 1.3 76.3 - - - +
986A SER* 1.3 53.1 + - - +
988A ILE* 3.0 24.7 + - - +
989A ASP* 2.7 66.4 + - - +
1027A ARG* 3.0 46.5 + - - +
1028A PHE* 5.9 0.8 - - - -
1031A LEU* 4.3 3.6 - - - +
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Residues in contact with SER 986 (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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605A HIS* 4.4 20.7 - - - -
608A ALA* 5.0 4.9 - - - -
953A PHE* 3.8 32.8 - - - -
984A ALA 3.3 0.6 - - - -
985A GLN* 1.3 74.6 - - - +
987A ILE* 1.3 54.4 + - - +
989A ASP* 4.6 3.4 - - - -
990A GLU* 2.8 44.8 + - - +
991A PHE* 5.0 0.4 - - - -
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Residues in contact with ILE 987 (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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608A ALA* 3.4 26.0 - - + +
611A PRO* 4.4 0.4 - - + -
612A VAL* 4.2 1.3 - - + -
953A PHE* 3.6 43.7 - - + +
956A VAL* 3.7 24.5 - - + +
957A GLY* 3.8 23.3 - - - +
960A TYR* 4.4 3.4 - - + -
984A ALA 3.1 9.6 + - - +
986A SER* 1.3 72.3 - - - +
988A ILE* 1.4 61.1 + - - +
991A PHE* 2.9 49.1 + - + -
992A ILE* 3.0 20.8 + - + -
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Residues in contact with ILE 988 (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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956A VAL* 4.8 1.1 - - + -
981A VAL* 3.7 38.8 - - + +
984A ALA* 3.1 18.3 + - + +
985A GLN* 3.0 21.1 + - - +
987A ILE* 1.4 77.4 - - - +
989A ASP* 1.3 53.8 + - - +
992A ILE* 4.1 17.5 - - + -
993A SER* 2.8 39.3 + - - +
1007A LEU* 4.4 13.9 - - + -
1028A PHE* 3.6 33.4 - - + -
1031A LEU* 3.8 19.5 - - + -
1037A MET* 5.8 0.4 - - - -
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Residues in contact with ASP 989 (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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985A GLN* 2.7 55.2 + - - +
986A SER* 4.0 3.0 - - - +
988A ILE* 1.3 71.8 - - - +
990A GLU* 1.3 67.5 + - + +
991A PHE 3.7 0.2 - - - -
993A SER* 3.3 10.7 + - - -
994A SER* 2.7 25.1 + - - -
998A LYS* 4.5 0.5 + - - -
1031A LEU* 3.8 20.1 - - + +
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Residues in contact with GLU 990 (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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603A PRO* 3.5 26.8 - - + +
605A HIS* 3.3 47.3 + - + +
986A SER* 2.8 27.6 + - - +
989A ASP* 1.3 83.6 - - + +
991A PHE* 1.3 62.5 + - + +
994A SER* 3.4 7.7 + - - -
998A LYS* 2.8 33.2 + - - +
999A TRP* 3.2 13.9 - - - -
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Residues in contact with PHE 991 (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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601A ALA 4.1 14.8 - - - -
603A PRO* 3.3 34.1 - - + -
608A ALA* 3.8 12.8 - - + -
609A VAL* 3.7 21.8 - - + -
612A VAL* 3.9 13.0 - - + -
960A TYR* 3.5 43.4 - + + -
987A ILE* 2.9 46.9 + - + +
989A ASP 3.7 0.2 - - - -
990A GLU* 1.3 83.5 - - + +
992A ILE* 1.3 62.0 + - - +
993A SER 3.6 0.7 - - - -
995A GLY* 2.8 29.9 + - - +
999A TRP* 3.7 16.8 - + - -
1001A GLN* 4.8 0.4 - - - -
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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