Contacts of the helix formed by residues 805 - 812 (chain B) in PDB entry 5MQF
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 GLY 805 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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765B SER* 5.8 4.0 - - - -
804B GLY* 1.3 72.8 - - - -
806B GLY* 1.3 56.5 + - - +
808B ILE* 4.7 1.6 - - - -
809B ILE* 2.9 39.6 + - - +
810B PRO* 3.2 1.6 - - - +
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Residues in contact with GLY 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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679B PRO* 4.7 7.7 - - - +
804B GLY 3.2 0.6 - - - -
805B GLY* 1.3 76.5 - - - +
807B GLN* 1.3 57.5 + - - +
808B ILE 3.4 0.4 - - - -
810B PRO* 3.1 25.3 - - - +
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Residues in contact with GLN 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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678B THR* 3.8 22.5 - - - -
679B PRO* 3.7 27.8 - - + -
680B ASN* 5.4 1.6 - - + +
683B ASN* 5.3 3.5 - - - +
802B HIS 4.7 3.6 - - - +
803B ARG* 3.8 14.8 - - - +
804B GLY 3.2 22.5 + - - +
806B GLY* 1.3 75.5 - - - +
808B ILE* 1.3 58.1 + - - +
810B PRO* 4.8 0.2 - - - -
811B THR* 4.1 12.3 - - - -
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Residues in contact with ILE 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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683B ASN* 6.2 2.9 - - + -
765B SER* 3.8 28.3 - - - -
766B ILE* 5.0 2.3 - - - +
803B ARG* 5.7 3.1 - - + -
804B GLY 3.2 16.4 + - - +
805B GLY* 4.7 0.4 - - - -
806B GLY 3.4 1.2 - - - -
807B GLN* 1.3 78.8 - - - +
809B ILE* 1.3 67.9 + - - +
810B PRO* 3.4 1.6 - - - -
811B THR* 3.0 6.2 + - - -
812B ALA* 3.0 22.2 + - - +
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Residues in contact with ILE 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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765B SER* 3.9 9.6 + - - +
768B GLN* 4.6 5.2 - - + -
769B GLY* 3.3 41.5 - - - +
805B GLY* 2.9 25.4 + - - +
808B ILE* 1.3 75.7 - - - +
810B PRO* 1.3 63.1 - - + +
812B ALA* 3.2 8.9 + - - +
813B ARG* 3.9 2.1 + - - +
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Residues in contact with PRO 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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805B GLY 3.2 13.2 - - - +
806B GLY* 3.1 25.1 - - - +
808B ILE 3.6 0.7 - - - -
809B ILE* 1.3 91.9 - - + +
811B THR* 1.3 61.5 + - - +
812B ALA 3.4 0.5 + - - -
813B ARG* 3.4 15.3 + - + +
814B ARG* 3.6 9.7 + - - +
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Residues in contact with THR 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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676B ALA* 4.6 13.7 - - - +
677B GLU 5.0 12.1 - - - -
678B THR* 5.8 0.2 - - - -
679B PRO* 6.2 0.7 - - - -
685B ILE* 5.3 5.9 - - - +
807B GLN 4.1 17.0 - - - -
808B ILE* 3.0 10.4 + - - -
810B PRO* 1.3 78.8 - - - +
812B ALA* 1.3 64.1 + - - +
813B ARG 3.3 0.2 - - - -
814B ARG* 3.3 10.3 + - - +
815B VAL* 3.2 22.3 + - - +
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Residues in contact with ALA 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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685B ILE* 5.9 3.6 - - - -
766B ILE* 3.5 36.6 - - + +
769B GLY 5.2 0.4 - - - -
770B PHE* 4.0 11.8 - - + +
808B ILE 3.0 9.9 + - - +
809B ILE 3.5 11.2 - - - +
810B PRO 3.2 0.6 - - - -
811B THR* 1.3 78.9 - - - +
813B ARG* 1.3 57.2 + - - +
815B VAL* 3.6 5.4 + - - +
816B VAL* 3.1 26.9 + - - +
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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