Contacts of the helix formed by residues 800 - 808 (chain B) in PDB entry 4DQL
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 800 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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756B LEU 4.5 3.0 + - - -
757B GLN* 3.6 33.2 - - + +
758B ASP 3.4 21.1 - - - +
760B VAL* 3.9 4.3 - - - -
798B ARG 3.4 17.0 - - - +
799B LEU* 1.3 73.9 - - - +
801B MET* 1.3 64.4 + - - +
802B LEU* 3.5 6.9 + - - +
803B GLU* 3.0 39.5 + - - +
804B LEU* 3.1 25.3 + - - +
861B TYR* 6.3 0.4 - - + -
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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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758B ASP 4.4 2.0 + - - -
760B VAL* 3.7 16.5 - - + +
764B GLN* 3.8 42.8 - - + +
768B MET* 4.0 14.8 - - + -
800B THR* 1.3 70.0 - - - +
802B LEU* 1.3 66.0 + - - +
804B LEU* 3.0 3.6 + - - +
805B LEU* 3.0 31.9 + - + +
813B MET* 4.0 27.6 - - - +
818B PHE* 3.5 32.3 - - + +
821B LEU* 4.0 5.4 - - + -
822B LEU* 3.6 26.5 - - + -
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Residues in contact with LEU 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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711B ILE* 3.8 31.6 - - + -
714B ARG* 3.9 34.3 - - + +
715B VAL* 4.1 33.9 - - + -
718B ARG* 4.8 9.0 - - + -
719B PHE* 5.7 0.9 - - + -
756B LEU* 4.2 12.9 + - + +
800B THR* 3.3 7.4 + - - +
801B MET* 1.3 75.3 - - - +
803B GLU* 1.3 65.0 + - - +
805B LEU* 3.2 10.1 + - + +
806B GLU* 3.0 34.8 + - + +
818B PHE* 4.5 15.1 - - + -
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Residues in contact with GLU 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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714B ARG* 3.5 22.5 + - - +
798B ARG 3.7 2.3 - - - +
799B LEU* 3.4 5.3 - - + +
800B THR* 3.0 46.1 + - - +
802B LEU* 1.3 77.7 - - - +
804B LEU* 1.3 57.3 + - - +
806B GLU* 3.2 9.5 + - - +
807B LYS* 2.9 21.7 + - - +
854B ALA* 4.4 5.2 - - - +
856B SER* 2.6 39.5 + - - -
858B TYR* 3.4 39.6 - - + +
861B TYR* 5.8 2.3 - - - -
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Residues in contact with LEU 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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760B VAL* 3.7 29.6 - - + -
765B LEU* 3.9 18.8 - - + -
768B MET* 3.9 18.2 - - + -
781B LEU* 4.4 1.6 - - + -
784B LEU* 4.2 10.3 - - + -
799B LEU* 3.9 30.5 - - + -
800B THR 3.1 12.5 + - - +
801B MET 3.0 7.6 + - - +
803B GLU* 1.3 75.0 - - - +
805B LEU* 1.3 59.9 + - - +
807B LYS* 3.2 15.6 + - + -
808B TYR* 2.9 55.5 + - + +
858B TYR* 4.8 0.9 - - - +
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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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718B ARG* 2.8 50.0 + - + +
719B PHE* 3.9 16.4 - - + -
768B MET* 4.2 11.9 - - + -
801B MET* 3.0 24.4 + - + +
802B LEU* 3.6 8.7 - - + +
804B LEU* 1.3 75.6 - - - +
806B GLU* 1.3 61.6 + - - +
808B TYR* 3.2 15.6 - - - -
809B PRO 3.4 0.5 - - - -
811B CYS* 4.0 23.6 - - + -
813B MET* 4.5 12.3 - - + -
818B PHE* 3.6 36.3 - - + -
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Residues in contact with GLU 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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714B ARG* 2.8 63.7 + - - +
718B ARG* 4.6 13.2 - - + +
802B LEU* 3.0 25.5 + - + +
803B GLU* 3.2 11.6 + - - +
805B LEU* 1.3 76.8 - - - +
807B LYS* 1.3 60.9 + - - +
808B TYR 3.4 0.3 + - - -
809B PRO* 3.5 13.3 - - - +
858B TYR* 4.3 12.5 - - + -
1105B PG4 4.3 7.8 - - - +
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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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777B HIS* 5.6 1.7 - - - -
780B GLU* 4.6 5.1 + - - -
803B GLU 2.9 7.8 + - - +
804B LEU* 3.2 20.8 + - + +
806B GLU* 1.3 76.1 - - - +
808B TYR* 1.3 97.6 + - + +
809B PRO* 3.2 8.3 - - - +
858B TYR* 3.3 29.1 - - - +
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Residues in contact with TYR 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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718B ARG* 3.1 10.2 + - - -
768B MET* 5.8 1.1 - - - -
772B THR* 5.7 1.8 - - + +
777B HIS* 3.5 47.3 - + + +
780B GLU* 2.6 42.8 + - + +
781B LEU* 3.8 33.7 - - + -
784B LEU* 6.1 1.0 - - + +
804B LEU* 2.9 34.9 + - + +
805B LEU 3.2 5.5 - - - +
807B LYS* 1.3 110.6 - - + +
809B PRO* 1.3 65.2 - - - +
810B ALA 3.1 2.9 - - - +
811B CYS* 3.0 27.2 + - + +
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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