Contacts of the helix formed by residues 798 - 812 (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 798 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788B TYR* 4.1 22.9 - - - -
795B HIS 4.8 3.7 + - - -
796B MET 5.3 0.2 + - - -
797B ASN* 1.3 75.8 - - - +
799B PRO* 1.3 76.2 - - - +
800B GLU* 3.2 25.1 - - - +
801B MET* 3.1 16.1 - - - +
802B SER* 3.0 25.6 + - - -
833B TYR* 5.6 1.0 - - - -
1139B MET* 3.9 6.0 - - - +
1141B ARG* 5.0 0.7 - - - +
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Residues in contact with PRO 799 (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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788B TYR* 4.8 12.1 - - + -
798B SER* 1.3 86.2 - - - +
800B GLU* 1.3 72.4 + - - +
802B SER* 3.2 3.1 + - - -
803B LYS* 3.0 49.3 + - - +
1138B ILE 3.4 25.1 - - - +
1139B MET* 4.0 12.3 - - + +
1140B ALA* 5.8 0.4 - - - -
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Residues in contact with GLU 800 (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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788B TYR* 3.1 37.6 + - + -
798B SER* 3.2 12.7 - - - +
799B PRO* 1.3 94.5 - - - +
801B MET* 1.3 66.8 + - - +
803B LYS* 3.4 8.6 + - - +
804B SER* 3.2 21.8 + - - -
833B TYR* 3.5 36.4 + - + +
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Residues in contact with MET 801 (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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796B MET 4.2 9.0 - - - +
797B ASN* 3.3 21.1 - - + +
798B SER* 3.1 39.3 - - - +
800B GLU* 1.3 79.8 - - - +
802B SER* 1.3 90.6 + - - +
804B SER* 3.0 15.9 + - - -
805B LEU* 3.1 7.6 + - - +
830B TYR* 3.7 31.2 - - + -
833B TYR* 3.6 33.1 - - + -
834B LEU* 4.5 3.8 - - + -
1109B LYS* 4.1 12.1 - - - -
1130B ILE* 6.2 1.1 - - - -
1133B ILE* 3.8 8.5 - - + -
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Residues in contact with SER 802 (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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798B SER 3.0 13.7 + - - -
799B PRO 3.4 8.5 - - - -
801B MET* 1.3 91.2 - - - +
803B LYS* 1.3 57.2 + - - +
805B LEU* 3.3 4.7 + - - +
806B HIS* 3.0 28.0 + - - +
1133B ILE* 3.4 26.5 - - - +
1137B CYS 3.6 19.9 - - - +
1138B ILE* 4.1 9.2 - - - -
1139B MET* 3.5 9.5 - - - +
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Residues in contact with LYS 803 (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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799B PRO* 3.0 40.8 + - - +
800B GLU* 3.9 7.4 - - - +
802B SER* 1.3 74.0 - - - +
804B SER* 1.3 62.7 + - - +
806B HIS* 3.5 6.9 + - - +
807B LYS* 3.3 43.7 + - - +
1138B ILE* 4.0 36.9 - - + +
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Residues in contact with SER 804 (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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800B GLU 3.2 13.2 + - - -
801B MET 3.0 13.3 + - - -
803B LYS* 1.3 74.3 - - - +
805B LEU* 1.3 65.4 + - - +
807B LYS* 3.5 5.8 + - - +
808B ALA* 3.2 17.7 + - - +
826B HIS* 3.5 30.2 - - - +
829B LEU* 4.5 11.4 - - - -
830B TYR* 3.4 20.6 - - - +
833B TYR* 3.9 8.6 - - - -
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Residues in contact with LEU 805 (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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801B MET* 3.1 9.7 + - - +
802B SER 3.3 8.7 + - - +
804B SER* 1.3 76.7 + - - +
806B HIS* 1.3 63.0 + - - +
808B ALA* 3.2 3.1 + - - +
809B VAL* 3.1 26.7 + - + +
827B TYR* 3.9 29.6 - - + -
830B TYR* 3.6 39.9 - - + +
1130B ILE* 4.1 11.4 - - + +
1133B ILE* 3.8 22.4 - - + -
1134B ALA* 4.7 6.7 - - - +
1173B PHE* 4.0 31.2 - - + -
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Residues in contact with HIS 806 (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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802B SER 3.0 15.8 + - - +
803B LYS* 4.0 8.5 - - - +
804B SER 3.3 0.4 - - - -
805B LEU* 1.3 78.2 - - - +
807B LYS* 1.3 58.7 + - + +
809B VAL* 3.5 5.1 + - - +
810B ALA* 2.9 33.4 + - + +
1133B ILE 3.6 12.1 + - - +
1134B ALA* 3.1 18.3 + - - +
1135B GLU 3.8 2.5 - - - -
1136B GLY* 3.6 20.8 - - - -
1137B CYS 6.0 0.2 - - - +
1164B LYS* 4.4 27.5 + - - +
1169B GLN* 2.9 37.9 + - + -
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Residues in contact with LYS 807 (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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803B LYS* 3.3 30.4 + - - +
804B SER* 4.1 1.7 - - - +
805B LEU 3.2 0.6 - - - -
806B HIS* 1.3 78.0 - - + +
808B ALA* 1.3 66.0 + - - +
810B ALA* 3.8 6.7 - - + +
811B ALA* 3.1 25.5 + - - +
826B HIS* 3.3 43.3 - - + +
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Residues in contact with ALA 808 (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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804B SER 3.2 8.8 + - - +
805B LEU* 3.2 10.2 + - - +
807B LYS* 1.3 77.3 - - - +
809B VAL* 1.3 61.8 + - - +
810B ALA 3.5 0.2 + - - -
811B ALA* 3.5 11.0 + - - +
812B TYR 3.8 8.8 + - - +
825B ASP* 4.3 7.4 - - - +
826B HIS* 3.4 7.9 - - - +
827B TYR* 3.4 49.6 - - + +
1176B PHE* 4.0 15.2 - - + -
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Residues in contact with VAL 809 (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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805B LEU* 3.1 14.5 + - + +
806B HIS* 3.7 9.6 - - - +
808B ALA* 1.3 80.3 - - - +
810B ALA* 1.3 63.1 + - - +
812B TYR 4.1 1.1 + - - -
1134B ALA* 3.6 17.7 - - + +
1169B GLN* 3.2 49.4 - - + +
1172B ASN* 3.5 24.9 + - - -
1173B PHE* 3.6 33.7 - - + +
1176B PHE* 4.0 13.7 - - + -
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Residues in contact with ALA 810 (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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806B HIS* 2.9 28.1 + - + +
807B LYS* 3.8 8.3 - - + +
808B ALA 3.3 0.4 - - - -
809B VAL* 1.3 79.2 - - + +
811B ALA* 1.3 63.2 + - - +
812B TYR* 3.6 1.2 + - - -
1169B GLN* 4.7 10.1 - - + +
1172B ASN* 5.7 0.2 + - - -
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Residues in contact with ALA 811 (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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807B LYS 3.1 17.0 + - - +
808B ALA* 3.5 6.7 + - - +
809B VAL 3.4 0.4 - - - -
810B ALA* 1.3 78.2 - - - +
812B TYR* 1.3 64.5 + - - +
825B ASP* 5.8 4.9 - - - +
826B HIS* 5.3 6.5 - - + -
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Residues in contact with TYR 812 (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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808B ALA 3.8 7.5 + - - +
809B VAL 4.4 1.8 - - - -
810B ALA 3.4 3.6 - - - -
811B ALA* 1.3 82.5 - - - +
1172B ASN* 3.4 43.2 - - - +
1176B PHE* 4.2 16.9 - - - -
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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