Contacts of the helix formed by residues 953 - 960 (chain A) in PDB entry 1OFD
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 THR 953 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951A GLY 3.2 11.4 + - - -
952A VAL* 1.3 74.4 - - - +
954A PRO* 1.3 69.0 - - - +
955A GLU* 3.9 0.9 - - + -
956A TYR* 3.2 23.0 + - + +
957A LEU* 3.0 26.1 + - - +
993A ARG* 3.7 17.4 + - - +
1294A ASN* 2.8 31.5 + - - +
1316A PHE* 4.9 1.6 - - - -
1336A GLY 5.4 0.2 - - - -
1338A ASN* 3.7 15.9 + - - -
1369A THR* 3.7 9.0 + - - +
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Residues in contact with PRO 954 (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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953A THR* 1.3 81.4 - - + +
955A GLU* 1.3 61.2 + - - +
957A LEU* 3.1 4.6 + - + +
958A MET* 2.9 26.5 + - - +
1025A ILE* 4.0 20.6 - - + -
1285A SER* 5.0 1.1 - - - +
1289A ALA* 3.8 20.4 - - + -
1294A ASN* 3.2 16.2 - - - +
1316A PHE* 3.4 31.6 - - + +
1318A LEU* 3.5 17.0 - - + -
1336A GLY 4.7 2.7 - - - +
1338A ASN* 3.6 21.1 - - + -
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Residues in contact with GLU 955 (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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908A VAL* 3.6 33.1 - - + +
911A TYR* 3.8 19.3 - - + -
953A THR* 3.3 0.9 - - + -
954A PRO* 1.3 72.9 - - - +
956A TYR* 1.3 61.9 + - - +
958A MET* 3.2 5.5 + - - +
959A SER* 3.1 22.3 + - - -
1289A ALA* 4.0 10.5 - - - +
1293A GLY* 3.5 20.2 - - - -
1294A ASN* 2.9 50.2 + - - +
1295A ASN* 5.5 1.2 + - - -
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Residues in contact with TYR 956 (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 SER* 3.0 19.4 + - - -
902A GLY 3.7 6.1 + - - -
903A GLU* 5.4 0.2 - - - -
905A GLY* 3.6 26.3 + - - -
906A GLU* 3.8 7.6 - - + -
911A TYR* 3.4 28.0 + - - +
943A LYS* 3.5 40.7 - - + +
944A GLN 2.7 30.1 + - - -
951A GLY* 3.5 22.4 + - - +
952A VAL* 4.0 17.3 - - + -
953A THR* 3.2 20.0 + - + +
955A GLU* 1.3 77.8 - - - +
957A LEU* 1.3 78.0 + - + +
959A SER* 2.8 20.3 + - - -
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Residues in contact with LEU 957 (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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945A ILE* 3.7 35.2 - - + -
952A VAL* 4.1 5.8 - - + -
953A THR 3.0 14.9 + - - +
954A PRO 3.6 6.5 - - - +
956A TYR* 1.3 91.4 - - + +
958A MET* 1.3 59.3 + - - +
959A SER 3.5 0.3 + - - -
960A GLY 3.6 2.6 + - - -
963A LEU* 3.6 26.4 - - + +
1022A LEU* 4.2 12.3 - - + -
1025A ILE* 4.2 23.1 - - + -
1026A ASN* 3.1 17.6 + - - -
1316A PHE* 3.7 44.9 - - + -
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Residues in contact with MET 958 (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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954A PRO 2.9 20.0 + - - +
955A GLU* 3.2 6.7 + - - +
957A LEU* 1.3 75.0 - - - +
959A SER* 1.3 61.3 + - - +
960A GLY 3.3 2.4 + - - +
1025A ILE* 3.3 34.8 - - - +
1026A ASN* 3.8 33.6 + - - +
1027A PRO* 5.3 2.0 - - + -
1286A GLY* 3.4 33.7 - - - +
1287A ALA* 5.3 0.2 - - - -
1289A ALA* 3.9 12.1 - - + +
1290A LYS* 3.9 33.4 - - + +
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Residues in contact with SER 959 (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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911A TYR* 3.5 32.6 - - - -
939A ASN* 3.0 25.5 + - - +
940A SER 4.2 0.5 - - - +
943A LYS* 2.9 21.0 + - - -
955A GLU 3.1 13.0 + - - -
956A TYR 2.8 15.1 + - - -
958A MET* 1.3 76.4 - - - +
960A GLY* 1.3 60.9 + - - +
961A LYS* 3.8 1.7 + - - +
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Residues in contact with GLY 960 (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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940A SER 4.4 0.9 - - - -
941A ALA 3.6 9.6 - - - -
943A LYS* 3.9 15.7 - - - -
956A TYR 3.6 2.2 + - - -
957A LEU 3.6 7.4 + - - -
958A MET 3.3 2.5 - - - +
959A SER* 1.3 82.0 + - - +
961A LYS* 1.3 64.6 + - - -
962A GLN 3.2 7.2 - - - -
963A LEU* 4.5 0.9 - - - -
1026A ASN* 3.4 22.0 + - - -
1029A ALA* 4.1 1.3 - - - +
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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