Contacts of the helix formed by residues 953 - 960 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908B VAL* 6.2 2.2 - - + -
911B TYR* 6.2 0.2 - - + -
951B GLY 3.2 12.3 + - - -
952B VAL* 1.3 73.4 - - - +
954B PRO* 1.3 69.0 - - - +
955B GLU* 3.4 2.0 - - + +
956B TYR* 3.2 24.0 + - + +
957B LEU* 3.1 25.9 + - - +
993B ARG* 3.7 17.8 + - - +
1294B ASN* 2.9 34.5 + - - +
1316B PHE* 4.7 0.9 - - - -
1338B ASN* 3.7 11.3 + - - -
1369B THR* 3.8 8.1 - - - +
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Residues in contact with PRO 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953B THR* 1.3 81.4 - - - +
955B GLU* 1.3 57.7 + - - +
957B LEU* 3.3 4.6 + - + +
958B MET* 2.9 32.7 + - - +
1025B ILE* 4.0 19.3 - - + -
1285B SER 4.9 0.9 - - - +
1289B ALA* 3.9 13.5 - - + -
1294B ASN* 3.3 15.5 - - - +
1316B PHE* 3.4 36.1 - - + +
1318B LEU* 3.6 20.9 - - + -
1336B GLY 4.6 0.7 - - - +
1338B ASN* 3.5 20.6 - - + -
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Residues in contact with GLU 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B VAL* 3.4 30.6 - - + +
911B TYR* 3.8 17.8 - - + -
953B THR* 4.8 0.7 - - + -
954B PRO* 1.3 73.2 - - - +
956B TYR* 1.3 57.9 + - - +
958B MET* 3.7 5.3 - - - +
959B SER* 2.9 28.2 + - - -
1289B ALA* 4.0 8.7 - - + +
1293B GLY* 3.4 22.7 - - - -
1294B ASN* 2.9 51.4 + - - +
1295B ASN* 5.7 0.5 + - - -
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Residues in contact with TYR 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901B SER* 3.0 18.5 + - - -
902B GLY 3.7 6.2 + - - -
903B GLU* 5.3 0.7 - - - -
905B GLY* 3.6 26.2 + - - -
906B GLU* 3.7 10.1 - - + -
911B TYR* 3.4 26.2 + - - +
943B LYS* 3.3 37.9 - - + +
944B GLN 2.6 29.0 + - - -
951B GLY* 3.6 21.2 + - - +
952B VAL* 3.9 20.1 - - + +
953B THR* 3.2 24.4 - - + +
955B GLU* 1.3 76.0 - - - +
957B LEU* 1.3 74.0 + - + +
959B SER* 2.6 20.5 + - - -
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Residues in contact with LEU 957 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945B ILE* 3.7 35.0 - - + -
952B VAL* 4.1 9.0 - - + -
953B THR 3.1 14.9 + - - +
954B PRO 3.3 5.8 + - - +
956B TYR* 1.3 82.6 - - + +
958B MET* 1.3 59.8 + - - +
960B GLY 3.5 6.8 + - - -
963B LEU* 3.6 23.0 - - + +
1022B LEU* 4.1 9.2 - - + -
1025B ILE* 4.1 29.4 - - + -
1026B ASN* 3.1 18.4 + - - -
1316B PHE* 3.7 44.0 - - + -
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Residues in contact with MET 958 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954B PRO 2.9 19.7 + - - +
955B GLU* 3.8 7.4 - - - +
956B TYR 3.2 0.2 - - - -
957B LEU* 1.3 77.2 - - - +
959B SER* 1.3 61.4 + - - +
960B GLY 3.2 2.5 + - - +
1025B ILE* 3.4 35.9 - - - +
1026B ASN* 3.8 32.8 + - - +
1027B PRO* 5.3 1.3 - - + -
1286B GLY* 3.4 32.5 - - - +
1287B ALA* 5.4 0.2 - - - -
1289B ALA* 4.0 11.7 - - + +
1290B LYS* 4.0 34.0 - - + +
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Residues in contact with SER 959 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911B TYR* 3.4 34.7 - - - -
939B ASN* 3.1 25.1 + - - +
940B SER 4.1 0.5 - - - +
943B LYS* 2.9 21.7 + - - -
955B GLU 2.9 13.3 + - - -
956B TYR 2.6 18.2 + - - -
958B MET* 1.3 76.7 - - - +
960B GLY* 1.3 59.7 + - - +
961B LYS* 3.8 2.3 + - - +
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Residues in contact with GLY 960 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940B SER 4.4 0.9 - - - -
941B ALA 3.6 9.2 - - - -
943B LYS* 3.9 17.5 - - - -
956B TYR 3.5 1.6 + - - -
957B LEU 3.5 6.8 + - - +
958B MET 3.2 2.4 - - - +
959B SER* 1.3 82.9 + - - +
961B LYS* 1.3 64.1 + - - -
962B GLN 3.2 6.5 - - - -
963B LEU* 4.5 1.5 - - - +
1026B ASN* 3.4 22.2 + - - -
1029B ALA* 4.0 1.7 - - - +
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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
------------------------------------------------------------
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