Contacts of the helix formed by residues 799 - 807 (chain B) in PDB entry 1UKJ
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 GLN 799 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B ALA* 3.8 14.4 - - - +
664B MET 4.8 0.8 + - - -
665B HIS* 3.4 22.3 + - - +
666B MET* 3.2 47.1 - - + +
797B PHE* 2.8 19.4 + - + -
798B PRO* 1.3 84.8 - - + +
800B TYR* 1.3 65.8 + - - +
801B THR 3.4 2.0 - - - -
802B LEU* 3.4 24.2 + - + +
803B ALA* 3.0 20.3 + - - +
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Residues in contact with TYR 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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792B PRO 3.9 14.1 - - - -
793B GLY* 4.2 8.4 + - - -
794B LEU 3.1 27.8 - - - -
795B ALA* 3.7 28.4 - - + +
797B PHE* 2.7 27.7 + - - +
798B PRO 3.4 2.6 + - - +
799B GLN* 1.3 72.3 - - - +
801B THR* 1.3 73.1 + - - +
803B ALA* 3.1 4.8 + - - +
804B ARG* 3.1 61.9 + - - +
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Residues in contact with THR 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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799B GLN 3.4 0.4 - - - -
800B TYR* 1.3 86.3 - - - +
802B LEU* 1.3 66.5 + - - +
804B ARG* 3.2 15.6 + - - +
805B GLN* 3.3 29.2 + - - +
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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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638B ALA* 5.6 1.8 - - + -
666B MET* 4.1 10.3 - - + -
667B ALA 3.4 27.8 - - - +
668B ASP* 4.3 18.8 - - + +
799B GLN* 3.4 35.1 + - + +
801B THR* 1.3 77.3 - - - +
803B ALA* 1.3 55.4 + - - +
805B GLN* 2.8 43.2 + - + +
806B GLN* 3.3 26.6 + - + +
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Residues in contact with ALA 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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666B MET* 4.1 33.8 - - + +
792B PRO* 4.7 12.6 - - + +
797B PHE* 4.8 0.7 - - + -
799B GLN 3.0 15.0 + - - +
800B TYR* 3.2 12.1 - - - +
802B LEU* 1.3 76.6 - - - +
804B ARG* 1.3 56.5 + - + +
805B GLN 3.1 0.9 + - - -
806B GLN* 3.1 2.6 + - - +
807B MET* 2.7 45.7 + - - +
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Residues in contact with ARG 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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792B PRO 5.6 2.9 - - - +
800B TYR* 3.1 60.8 + - + +
801B THR* 3.2 9.0 + - - +
803B ALA* 1.3 77.0 - - + +
805B GLN* 1.3 59.0 + - - +
806B GLN 3.4 0.4 - - - -
807B MET 3.9 16.2 - - - +
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Residues in contact with GLN 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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700B LEU* 5.1 6.8 - - - +
801B THR* 3.3 29.6 + - - +
802B LEU* 2.8 26.8 + - + +
804B ARG* 1.3 78.8 - - - +
806B GLN* 1.3 62.2 + - + +
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Residues in contact with GLN 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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658B SER* 4.0 13.3 + - - -
666B MET* 4.4 9.9 - - - +
667B ALA 2.8 19.9 + - - +
668B ASP* 3.5 3.5 - - - +
669B ILE* 2.7 44.6 + - - +
670B ALA 4.3 1.0 + - - -
694B LEU 3.6 2.3 - - - +
695B GLN* 3.1 36.7 + - - +
696B ARG 4.8 0.5 + - - -
700B LEU* 3.9 21.5 - - + +
802B LEU* 3.3 23.5 + - + +
803B ALA 3.1 4.1 + - - +
805B GLN* 1.3 85.2 - - + +
807B MET* 1.3 60.5 + - + +
808B SER 4.0 0.2 + - - -
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Residues in contact with MET 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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659B PRO* 4.1 11.9 - - + -
666B MET* 3.3 39.7 - - + +
690B CYS* 4.0 20.2 - - - -
694B LEU 3.1 5.8 - - - +
695B GLN* 3.4 19.3 - - - +
792B PRO* 4.7 2.7 - - + -
803B ALA* 2.7 28.4 + - - +
804B ARG* 3.9 16.1 - - - +
806B GLN* 1.3 74.9 - - + +
808B SER* 1.3 63.2 + - - +
809B GLN* 3.1 26.1 + - - +
810B PRO* 3.9 20.6 - - + +
811B GLY* 4.3 2.7 - - - +
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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