Contacts of the helix formed by residues 977 - 983 (chain A) in PDB entry 2XT6
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 PHE 977 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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907A THR* 4.0 15.0 - - + -
908A PHE* 3.5 17.0 - + - -
975A ALA* 3.3 13.2 - - - +
976A GLN* 1.3 99.5 - - + +
978A GLY* 1.3 59.5 + - - +
979A ASP* 2.9 19.6 + - - +
980A PHE* 3.1 33.0 + + + +
1010A PRO* 4.2 4.7 - - - -
1016A GLN* 3.8 16.6 - - - -
1019A ASP 4.2 1.1 - - - +
1020A HIS* 3.6 50.3 - + + -
1070A LYS* 3.6 32.1 - - + -
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Residues in contact with GLY 978 (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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975A ALA* 4.0 5.4 - - - -
977A PHE* 1.3 69.6 - - - +
979A ASP* 1.4 58.0 + - - +
980A PHE 3.2 0.2 - - - -
981A VAL* 3.2 27.5 - - - +
1009A LEU* 3.9 18.4 - - - -
1010A PRO* 2.9 25.2 + - - +
1022A SER 3.5 6.5 - - - +
1023A GLY* 3.5 18.0 - - - -
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Residues in contact with ASP 979 (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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977A PHE* 2.9 15.1 + - + +
978A GLY* 1.4 79.6 + - - +
980A PHE* 1.3 62.4 + - + +
981A VAL 3.5 0.4 - - - -
982A ASN* 3.2 24.5 + - - +
1010A PRO 4.3 2.1 - - - +
1018A PRO 3.2 11.2 - - - +
1019A ASP* 3.1 39.6 - - + +
1020A HIS* 3.2 0.9 + - - -
1021A THR 2.8 29.5 + - - -
1022A SER* 3.0 25.5 + - - +
1024A ARG* 5.7 2.9 + - - +
1206A PRO* 5.0 0.9 - - - +
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Residues in contact with PHE 980 (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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901A GLN* 5.6 2.0 - - - +
952A GLU* 3.4 33.7 - - + +
975A ALA* 5.7 1.1 - - + -
976A GLN* 4.4 13.7 - - + +
977A PHE* 3.1 47.5 + + + +
979A ASP* 1.3 79.9 - - - +
981A VAL* 1.4 57.7 + - - +
982A ASN* 3.0 15.2 + - - +
983A GLY* 3.1 12.6 + - - -
1019A ASP* 3.7 29.4 - - + -
1020A HIS* 4.0 14.6 - + - -
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Residues in contact with VAL 981 (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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952A GLU* 4.7 2.0 - - - -
956A VAL* 4.6 0.7 - - + -
973A TRP* 3.7 31.6 - - + -
975A ALA* 4.8 2.0 - - + +
977A PHE 4.3 1.4 + - - -
978A GLY 3.2 21.2 + - - +
980A PHE* 1.4 75.6 - - - +
982A ASN* 1.4 57.2 + - - +
983A GLY 3.1 1.6 - - - -
984A ALA* 2.9 28.0 + - + +
988A ILE* 3.7 23.0 - - + +
1007A LEU* 4.6 8.3 - - + -
1009A LEU* 3.7 23.8 - - + -
1023A GLY 4.4 7.4 - - - +
1028A PHE* 4.4 16.2 - - + -
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Residues in contact with ASN 982 (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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979A ASP 3.2 21.5 + - - +
980A PHE* 3.5 5.5 - - - +
981A VAL* 1.4 79.9 - - + +
983A GLY* 1.3 65.4 + - - +
984A ALA 3.1 2.3 + - - -
985A GLN* 3.3 27.3 + - - +
988A ILE* 5.5 0.2 - - - -
1024A ARG* 4.3 23.2 - - - +
1027A ARG* 4.1 20.3 - - - +
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Residues in contact with GLY 983 (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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952A GLU* 4.1 13.0 - - - -
953A PHE* 3.4 26.7 + - - +
980A PHE 3.1 13.8 + - - -
982A ASN* 1.3 80.4 + - - +
984A ALA* 1.4 55.6 + - - +
985A GLN 3.6 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