Contacts of the helix formed by residues 985 - 993 (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 SER 985 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982A LYS 4.9 1.5 + - - -
983A LYS 3.1 6.1 + - - -
984A VAL* 1.3 78.1 - - - +
986A GLU* 1.3 59.2 + - - +
987A TYR* 3.3 11.0 + - - +
988A ILE* 3.1 26.6 + - - +
989A ALA* 2.9 26.9 + - - +
996A PRO* 4.9 1.8 - - - -
1155A GLN* 4.6 19.4 + - - -
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Residues in contact with GLU 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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985A SER* 1.3 73.6 - - - +
987A TYR* 1.3 56.6 + - - +
989A ALA* 3.4 7.6 + - - +
990A MET* 3.0 30.5 + - - +
996A PRO* 4.5 21.3 - - + +
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Residues in contact with TYR 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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877A LEU* 3.6 30.7 - - + +
882A ARG* 3.2 45.2 + - + +
886A GLU* 4.5 1.7 + - - -
907A ASP* 2.7 39.3 + - - +
985A SER* 3.2 9.0 + - - +
986A GLU* 1.3 79.2 - - - +
988A ILE* 1.3 61.5 + - + +
990A MET* 3.3 18.6 + - + +
991A LEU* 2.5 51.9 + - + +
1155A GLN* 5.3 3.4 - - - -
1160A ARG* 6.2 3.4 - - - +
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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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877A LEU* 3.6 33.0 - - + +
878A GLY* 3.9 15.0 - - - +
979A LEU* 3.9 16.2 - - + -
983A LYS 3.5 15.9 - - - +
984A VAL* 4.1 9.4 - - + -
985A SER* 3.1 23.4 + - - +
987A TYR* 1.3 76.4 - - + +
989A ALA* 1.3 60.7 + - - +
991A LEU* 3.2 6.1 + - + +
992A ARG* 2.9 57.4 + - + +
1155A GLN* 4.0 13.5 - - - +
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Residues in contact with ALA 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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984A VAL* 4.1 3.8 - - + +
985A SER 2.9 18.5 + - - +
986A GLU 3.8 4.0 - - - +
987A TYR 3.3 0.2 - - - -
988A ILE* 1.3 74.4 - - - +
990A MET* 1.3 52.9 + - - +
993A ARG* 2.8 31.4 + - - -
994A SER* 3.0 36.5 + - - +
995A LYS 3.9 2.2 - - - -
996A PRO* 3.6 29.4 - - + -
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Residues in contact with MET 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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907A ASP* 4.9 8.7 - - - +
986A GLU 3.0 13.9 + - - +
987A TYR* 3.4 24.9 - - + +
988A ILE 3.2 0.2 - - - -
989A ALA* 1.3 74.3 - - - +
991A LEU* 1.3 88.9 + - + +
992A ARG 3.3 0.5 + - - -
993A ARG* 3.3 24.5 + - - +
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Residues in contact with LEU 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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877A LEU* 3.5 34.5 - - + -
904A GLY 3.8 21.0 - - - +
905A GLY* 5.1 1.4 - - - -
906A GLU* 4.8 7.1 + - - +
907A ASP* 4.4 21.5 - - + +
950A PHE 3.8 7.3 - - - +
951A GLY* 5.0 1.7 - - - -
987A TYR* 2.5 60.0 + - + +
988A ILE* 3.2 9.1 + - + +
990A MET* 1.3 92.4 - - + +
992A ARG* 1.3 60.8 + - + +
993A ARG* 3.0 25.3 + - - +
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Residues in contact with ARG 992 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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876A SER* 3.5 2.0 + - - -
878A GLY* 3.2 27.3 - - - +
903A GLU 4.3 0.2 + - - -
904A GLY* 3.4 30.6 + - - +
950A PHE* 3.6 55.6 - - + +
979A LEU* 3.7 13.4 - - - +
988A ILE* 2.9 31.5 + - + +
991A LEU* 1.3 78.1 - - + +
993A ARG* 1.3 72.3 + - - +
994A SER* 3.5 12.6 + - - +
1000A LEU* 3.5 23.2 - - - +
1386A ARG* 4.2 0.7 + - - -
1388A SER* 3.4 8.1 + - - -
3510A AKG 2.6 44.0 + - - -
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Residues in contact with ARG 993 (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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906A GLU 5.7 3.0 + - - -
950A PHE 4.9 3.1 + - - -
951A GLY 4.7 8.1 + - - -
953A THR* 3.7 23.8 + - - +
989A ALA 2.8 10.3 + - - -
990A MET* 3.3 13.2 + - - +
991A LEU* 3.0 24.2 + - - +
992A ARG* 1.3 77.0 - - - +
994A SER* 1.3 56.6 + - - +
1294A ASN* 4.5 10.3 - - - +
1338A ASN* 4.9 4.2 + - - -
1369A THR* 4.3 20.9 + - - -
1388A SER* 2.8 36.8 + - - +
1389A VAL* 4.1 18.8 - - + -
1406A THR* 3.0 9.7 + - - +
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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
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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