Contacts of the helix formed by residues 811 - 818 (chain B) in PDB entry 5QSY
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 ARG 811 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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752B ILE 3.6 16.8 + - - -
753B THR* 3.5 28.7 + - - +
755B GLY 3.9 10.9 + - - -
756B SER* 5.9 0.4 - - - +
757B PRO* 4.4 11.3 - - - +
806B LEU 3.9 13.0 - - - +
807B MET* 3.0 28.9 + - - +
808B THR 4.5 2.7 - - - +
809B GLY 3.6 13.2 - - - +
810B GLY* 1.3 79.6 - - - +
812B GLU* 1.3 62.5 + - - +
813B GLY* 3.2 7.0 + - - +
814B LEU* 3.6 33.7 + - + +
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Residues in contact with GLU 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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807B MET* 3.6 28.8 - - + +
808B THR* 4.7 3.1 - - - -
809B GLY 4.9 0.3 + - - -
810B GLY* 3.2 26.2 + - - +
811B ARG* 1.3 75.5 - - - +
813B GLY* 1.3 63.2 + - - +
814B LEU 3.1 3.6 + - - -
815B GLN* 3.2 23.6 + - + +
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Residues in contact with GLY 813 (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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759B LYS* 5.2 3.3 - - - -
762B LEU* 3.8 17.3 - - - +
811B ARG* 3.2 5.2 - - - +
812B GLU* 1.3 77.6 - - - +
814B LEU* 1.3 59.4 + - - +
815B GLN* 3.3 4.9 + - - +
816B PRO* 3.9 5.2 - - - +
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Residues in contact with LEU 814 (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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752B ILE* 3.8 15.3 - - + -
753B THR* 3.8 28.0 - - + -
757B PRO* 4.5 5.6 - - + -
762B LEU* 3.6 27.6 - - + -
806B LEU* 4.0 31.0 - - + +
807B MET* 4.5 5.3 - - + +
811B ARG* 3.6 39.0 + - + +
812B GLU 3.1 2.4 + - - -
813B GLY* 1.3 76.3 - - - +
815B GLN* 1.3 63.9 + - - +
816B PRO* 3.4 4.7 - - - -
817B LEU* 3.3 22.3 + - + +
818B VAL* 4.0 7.4 - - - +
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Residues in contact with GLN 815 (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 MET* 3.2 38.8 - - - +
812B GLU* 3.2 14.7 + - + +
813B GLY 3.3 0.9 - - - +
814B LEU* 1.3 75.4 - - - +
816B PRO* 1.4 66.8 - - + +
818B VAL* 3.1 37.0 + - - +
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Residues in contact with PRO 816 (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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759B LYS* 4.4 16.2 - - + -
762B LEU* 4.0 33.9 - - + +
763B LEU* 5.2 6.5 - - + -
766B ARG* 3.2 52.3 + - - +
813B GLY 3.9 7.2 - - - +
814B LEU 3.5 2.5 - - - -
815B GLN* 1.4 94.5 - - + +
817B LEU* 1.3 59.8 + - - +
818B VAL 3.3 3.3 + - - +
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Residues in contact with LEU 817 (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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749B LEU* 4.3 14.6 - - + -
752B ILE* 4.1 16.6 - - + -
762B LEU* 3.5 49.1 - - + +
765B LEU* 3.8 30.3 - - + -
766B ARG* 3.8 9.6 - - - +
769B VAL* 5.2 1.1 - - + -
802B PHE* 3.3 23.4 - - + +
806B LEU* 3.9 13.7 - - + -
814B LEU* 3.3 16.7 + - + +
815B GLN 3.3 1.6 + - - -
816B PRO* 1.3 76.4 - - - +
818B VAL* 1.3 64.0 + - - +
819B PHE* 3.2 17.2 - - + -
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Residues in contact with VAL 818 (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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766B ARG* 5.2 6.6 + - - -
802B PHE 4.3 5.4 - - - -
803B SER* 3.9 26.2 - - - +
804B HIS* 4.1 2.9 - - + +
806B LEU* 5.3 2.7 - - + -
807B MET* 4.1 20.0 - - + -
814B LEU 4.0 8.7 - - - +
815B GLN* 3.1 36.5 + - - +
816B PRO 4.2 4.3 - - - +
817B LEU* 1.3 78.9 - - - +
819B PHE* 1.3 70.8 + - - +
820B ASN* 3.8 25.6 - - - +
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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