Contacts of the helix formed by residues 798 - 812 (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 798 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788A TYR* 4.1 25.1 - - - -
795A HIS 4.9 4.0 - - - -
796A MET 4.3 0.2 - - - -
797A ASN* 1.3 76.0 - - - +
799A PRO* 1.3 75.8 - - - +
800A GLU* 3.7 15.1 - - - +
801A MET* 3.1 22.7 + - - +
802A SER* 3.0 25.5 + - - -
833A TYR* 5.3 2.4 - - - -
1139A MET* 4.1 5.4 - - - +
1141A ARG* 5.0 0.7 - - - +
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Residues in contact with PRO 799 (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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788A TYR* 4.7 11.0 - - + -
798A SER* 1.3 88.5 - - - +
800A GLU* 1.3 66.2 + - - +
802A SER* 3.2 4.4 + - - -
803A LYS* 2.9 51.4 + - - +
1138A ILE* 3.5 24.7 - - + +
1139A MET* 4.0 13.7 - - + +
1140A ALA* 5.8 0.9 - - - -
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Residues in contact with GLU 800 (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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788A TYR* 3.8 28.1 + - + +
798A SER* 3.7 11.1 + - - +
799A PRO* 1.3 88.5 - - - +
801A MET* 1.3 67.3 + - - +
803A LYS* 3.2 9.4 + - - +
804A SER* 2.9 25.3 + - - -
833A TYR* 3.7 32.9 - - + +
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Residues in contact with MET 801 (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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796A MET 4.0 8.3 - - - +
797A ASN* 3.3 21.1 - - + +
798A SER* 3.1 49.7 + - - +
800A GLU* 1.3 79.8 - - - +
802A SER* 1.3 78.2 + - - +
804A SER* 3.2 8.7 + - - -
805A LEU* 3.2 17.9 + - - +
830A TYR* 3.6 32.9 - - + -
833A TYR* 4.3 27.3 - - + -
834A LEU* 4.5 5.6 - - + -
1109A LYS* 4.1 10.1 - - - -
1130A ILE* 6.3 1.1 - - - -
1133A ILE* 4.1 9.6 - - + -
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Residues in contact with SER 802 (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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798A SER 3.0 18.1 + - - -
799A PRO* 3.3 10.3 - - - -
801A MET* 1.3 91.3 - - - +
803A LYS* 1.3 61.0 + - - +
805A LEU 3.4 1.2 + - - -
806A HIS* 3.2 23.8 + - - +
1133A ILE* 3.5 23.2 - - - +
1137A CYS 3.6 21.2 - - - +
1138A ILE* 4.1 7.9 - - - -
1139A MET* 3.3 16.8 - - - +
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Residues in contact with LYS 803 (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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799A PRO* 2.9 37.1 + - - +
800A GLU* 3.2 8.0 + - - +
802A SER* 1.3 75.4 - - - +
804A SER* 1.3 63.7 + - - +
806A HIS* 3.4 5.6 + - - +
807A LYS* 3.2 44.6 + - - +
1138A ILE* 4.0 36.5 - - + +
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Residues in contact with SER 804 (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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800A GLU 2.9 17.8 + - - -
801A MET* 3.2 11.1 + - - -
803A LYS* 1.3 75.0 - - - +
805A LEU* 1.3 63.9 + - - +
807A LYS* 3.6 1.5 + - - +
808A ALA* 3.1 19.1 + - - +
826A HIS* 3.2 38.0 - - - +
829A LEU* 4.6 10.1 - - - -
830A TYR* 4.0 10.2 - - - -
833A TYR* 4.0 11.7 - - - -
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Residues in contact with LEU 805 (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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801A MET* 3.2 8.4 + - - +
802A SER 3.8 7.2 - - - +
803A LYS 3.3 0.2 - - - -
804A SER* 1.3 75.5 - - - +
806A HIS* 1.3 60.0 + - - +
808A ALA* 3.1 5.4 + - - +
809A VAL* 3.0 33.5 + - + +
827A TYR* 3.8 15.0 - - + -
830A TYR* 3.7 46.3 - - + +
1130A ILE* 4.3 13.5 - - + +
1133A ILE* 3.6 23.8 - - + -
1134A ALA* 4.3 11.0 - - + +
1173A PHE* 3.8 36.8 - - + -
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Residues in contact with HIS 806 (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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802A SER 3.2 14.1 + - - +
803A LYS* 3.9 7.0 - - - +
804A SER 3.3 0.2 - - - -
805A LEU* 1.3 80.3 - - - +
807A LYS* 1.3 63.5 + - + +
809A VAL* 3.6 4.4 + - - +
810A ALA* 3.0 31.0 + - + +
1133A ILE 4.0 9.8 + - - +
1134A ALA* 3.2 15.1 + - - +
1135A GLU 3.8 2.2 - - - -
1136A GLY* 3.6 33.3 + - - -
1137A CYS 5.7 0.2 - - - +
1138A ILE* 6.5 1.1 - - + -
1164A LYS* 4.3 28.7 + - - +
1165A GLY* 5.1 2.5 - - - -
1169A GLN* 3.3 33.7 + - - -
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Residues in contact with LYS 807 (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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803A LYS* 3.2 34.2 + - - +
804A SER* 5.2 0.7 - - - +
805A LEU 3.2 0.4 - - - -
806A HIS* 1.3 82.8 - - + +
808A ALA* 1.3 63.7 + - - +
810A ALA* 3.9 5.8 - - - +
811A ALA* 3.2 25.3 + - - +
826A HIS* 3.7 38.9 + - + +
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Residues in contact with ALA 808 (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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804A SER 3.1 10.9 + - - +
805A LEU 3.1 9.6 + - - +
807A LYS* 1.3 78.8 - - - +
809A VAL* 1.3 60.8 + - - +
811A ALA* 3.3 13.6 + - - +
812A TYR 3.8 10.7 + - - +
825A ASP* 4.0 9.1 - - - +
826A HIS* 3.3 8.4 - - - +
827A TYR* 3.4 49.4 - - + +
1176A PHE* 4.4 6.6 - - + -
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Residues in contact with VAL 809 (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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805A LEU* 3.0 17.7 + - + +
806A HIS* 3.9 6.7 - - - +
808A ALA* 1.3 79.1 - - - +
810A ALA* 1.3 58.5 + - - +
811A ALA 3.2 1.2 + - - -
812A TYR 3.9 1.2 + - - -
1134A ALA* 3.8 16.8 - - - +
1169A GLN* 3.1 37.3 - - + +
1172A ASN* 3.2 27.9 + - + -
1173A PHE* 3.5 42.4 - - + +
1176A PHE* 3.8 20.0 - - + -
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Residues in contact with ALA 810 (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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806A HIS* 3.0 24.0 + - + +
807A LYS* 3.9 5.8 - - - +
808A ALA 3.4 0.4 - - - -
809A VAL* 1.3 74.6 - - - +
811A ALA* 1.3 59.4 + - - +
812A TYR* 3.5 0.8 - - - -
1169A GLN* 3.8 28.5 - - - +
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Residues in contact with ALA 811 (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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807A LYS 3.2 18.1 + - - +
808A ALA* 3.5 8.7 - - - +
809A VAL 3.2 0.6 - - - -
810A ALA* 1.3 80.2 - - - +
812A TYR* 1.3 66.1 + - - +
825A ASP* 5.4 5.2 - - - +
826A HIS* 5.0 8.1 - - + -
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Residues in contact with TYR 812 (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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808A ALA 3.8 5.4 + - - +
809A VAL 3.9 1.2 + - - +
810A ALA 3.5 2.4 - - - -
811A ALA* 1.3 83.8 - - - +
1172A ASN* 3.5 35.2 - - - +
1176A PHE* 3.6 25.0 - - - -
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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