Contacts of the helix formed by residues 985 - 993 (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 SER 985 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982B LYS 5.7 1.1 - - - -
983B LYS 3.0 10.9 + - - -
984B VAL* 1.3 75.1 - - - +
986B GLU* 1.3 59.6 + - - +
987B TYR* 3.3 11.0 + - - +
988B ILE* 3.1 25.0 + - - +
989B ALA* 2.9 27.3 + - - +
996B PRO* 4.8 1.8 - - - -
1155B GLN* 4.5 18.9 + - - +
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Residues in contact with GLU 986 (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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985B SER* 1.3 74.0 - - - +
987B TYR* 1.3 61.2 + - - +
989B ALA* 3.4 5.5 + - - +
990B MET* 3.1 24.5 + - - +
996B PRO* 3.1 32.4 - - + +
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Residues in contact with TYR 987 (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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877B LEU* 3.7 15.3 - - + +
882B ARG* 3.3 41.8 + - + +
886B GLU* 4.7 1.0 + - - -
907B ASP* 2.6 40.5 + - - +
985B SER* 3.1 8.4 + - - +
986B GLU* 1.3 79.7 - - - +
988B ILE* 1.3 72.4 + - + +
990B MET* 3.2 29.8 + - + +
991B LEU* 3.1 42.5 + - + +
1155B GLN* 5.3 3.8 - - - -
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Residues in contact with ILE 988 (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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877B LEU* 3.5 31.9 - - + -
878B GLY* 4.0 14.6 - - - +
979B LEU* 4.1 14.6 - - + -
983B LYS 3.5 15.7 - - - +
984B VAL* 4.1 9.9 - - + -
985B SER* 3.1 23.0 + - - +
987B TYR* 1.3 78.8 - - + +
989B ALA* 1.3 67.4 + - - +
991B LEU* 3.3 6.3 + - + +
992B ARG* 3.0 51.8 + - + +
1155B GLN* 4.0 15.0 - - - +
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Residues in contact with ALA 989 (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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984B VAL* 4.2 3.5 - - + +
985B SER 2.9 16.1 + - - +
986B GLU 3.8 4.7 - - - +
988B ILE* 1.3 76.6 - - - +
990B MET* 1.3 52.3 + - - +
993B ARG* 2.8 30.0 + - - -
994B SER* 2.9 38.4 + - - +
995B LYS 4.0 2.0 - - - -
996B PRO* 3.5 30.1 - - + -
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Residues in contact with MET 990 (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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907B ASP* 4.7 4.7 - - - +
986B GLU 3.1 13.2 + - - +
987B TYR* 3.3 41.5 - - + +
989B ALA* 1.3 75.1 - - - +
991B LEU* 1.3 81.5 + - + +
993B ARG* 3.4 22.5 + - - +
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Residues in contact with LEU 991 (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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877B LEU* 3.6 21.3 - - + -
904B GLY 3.9 20.5 - - - +
905B GLY* 5.0 0.9 - - - -
906B GLU* 4.3 6.9 + - - +
907B ASP* 3.8 36.3 - - + +
950B PHE 3.7 8.1 - - - +
951B GLY* 4.7 2.3 - - - -
987B TYR* 3.1 39.4 + - + +
988B ILE* 3.7 10.8 - - + +
990B MET* 1.3 99.5 - - + +
992B ARG* 1.3 59.7 + - + +
993B ARG* 3.0 25.3 + - - +
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Residues in contact with ARG 992 (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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876B SER* 3.4 10.9 + - - -
878B GLY 3.5 15.6 - - - +
904B GLY* 3.5 28.1 + - - +
950B PHE* 3.6 55.9 - - + +
979B LEU* 3.5 17.2 - - - +
988B ILE* 3.0 29.7 + - + +
991B LEU* 1.3 77.4 - - + +
993B ARG* 1.3 72.8 + - - +
994B SER* 3.4 11.5 + - - +
1000B LEU* 3.6 22.2 - - - +
1386B ARG* 4.2 0.7 + - - -
1388B SER* 3.5 8.1 + - - -
3510B AKG 2.7 43.6 + - - -
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Residues in contact with ARG 993 (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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906B GLU 5.8 2.0 + - - -
950B PHE 4.7 4.4 + - - -
951B GLY 4.4 10.5 + - - -
953B THR* 3.7 21.3 + - - +
989B ALA 2.8 10.7 + - - -
990B MET* 3.4 12.5 + - - +
991B LEU* 3.0 24.7 + - - +
992B ARG* 1.3 77.9 - - - +
994B SER* 1.3 56.0 + - - +
1294B ASN* 4.6 8.3 - - - +
1338B ASN* 4.9 2.6 + - - -
1369B THR* 3.1 25.4 + - - +
1388B SER* 3.0 35.0 + - - +
1389B VAL* 3.9 15.9 - - + -
1406B THR* 3.1 11.3 + - - +
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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