Contacts of the helix formed by residues 699 - 707 (chain B) in PDB entry 5IA0
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 ALA 699 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697B ASN 3.8 0.5 + - - +
698B GLY* 1.3 71.6 - - - -
700B LEU* 1.3 65.5 + - - +
701B ASP* 3.3 16.7 + - - +
702B LYS* 3.4 11.0 + - + +
703B PHE* 3.0 23.7 + - - +
743B ARG* 4.1 17.3 - - + +
745B ILE 3.4 7.0 - - - -
746B LEU* 3.9 7.4 - - + +
1001B A5B 4.9 13.5 + - - -
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Residues in contact with LEU 700 (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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698B GLY 3.6 0.6 + - - -
699B ALA* 1.3 73.7 - - - +
701B ASP* 1.3 64.1 + - - +
703B PHE* 3.4 3.0 + - + +
704B LEU* 3.0 50.1 + - + +
719B MET* 4.4 8.7 - - + -
723B ILE* 3.8 22.4 - - + -
742B ALA* 3.5 23.9 + - + +
745B ILE* 2.8 27.0 + - + +
747B VAL* 3.8 26.5 - - + -
753B CYS* 4.2 9.9 - - - -
806B VAL* 4.7 0.4 - - + -
810B VAL* 3.7 23.6 - - + -
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Residues in contact with ASP 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B ALA* 3.6 10.9 - - - +
700B LEU* 1.3 76.5 - - - +
702B LYS* 1.3 70.9 + - - +
704B LEU* 3.4 3.3 + - - +
705B ARG* 2.9 56.6 + - - +
742B ALA* 3.6 21.8 + - + +
743B ARG* 3.5 31.4 - - - +
809B GLU* 4.4 7.6 - - - +
814B GLY* 4.3 9.1 - - - -
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Residues in contact with LYS 702 (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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699B ALA* 3.4 14.1 + - + +
701B ASP* 1.3 87.3 + - - +
703B PHE* 1.3 65.4 + - - +
705B ARG* 3.3 18.8 + - + +
706B GLU* 3.0 43.0 + - + +
1001B A5B 2.8 35.1 + - - +
1008B EDO 6.2 0.2 - - - -
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Residues in contact with PHE 703 (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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697B ASN* 3.4 54.5 + - + +
699B ALA 3.0 18.2 + - - +
700B LEU* 3.6 7.0 - - + +
701B ASP 3.3 0.2 - - - -
702B LYS* 1.3 78.4 - - - +
704B LEU* 1.3 72.6 + - + +
706B GLU* 3.2 8.0 + - + +
707B LYS* 3.0 50.8 + - + +
711B PHE* 3.6 34.3 - + - -
719B MET* 4.6 3.6 - - + -
747B VAL* 4.1 21.3 - - + -
751B LEU* 4.0 13.9 - - + -
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Residues in contact with LEU 704 (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* 3.0 40.7 + - + +
701B ASP* 4.0 2.5 - - - +
703B PHE* 1.3 79.6 - - + +
705B ARG* 1.3 66.3 + - - +
707B LYS* 3.1 4.7 + - - +
708B ASP* 3.1 22.9 + - - -
711B PHE* 3.9 32.1 - - + -
716B LEU* 4.3 10.3 - - + -
719B MET* 4.4 4.3 - - - -
809B GLU 4.4 2.9 - - - +
810B VAL* 3.6 43.7 - - + +
813B TYR* 3.5 24.5 - - + +
814B GLY* 4.2 1.6 - - - +
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Residues in contact with ARG 705 (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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701B ASP* 2.9 53.7 + - - +
702B LYS* 3.7 17.7 - - + +
703B PHE 3.3 0.2 - - - -
704B LEU* 1.3 76.7 - - - +
706B GLU* 1.3 62.1 + - + +
708B ASP* 3.7 7.4 + - - +
809B GLU* 5.8 0.4 + - - -
813B TYR 3.3 19.3 - - - +
814B GLY 2.8 34.2 + - - +
815B GLU 5.3 0.8 - - - -
1004B EDO 3.6 20.3 + - - +
1006B EDO 3.5 12.6 + - - -
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Residues in contact with GLU 706 (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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702B LYS* 3.0 34.6 + - + +
703B PHE* 3.6 10.8 - - + +
704B LEU 3.2 0.2 - - - -
705B ARG* 1.3 78.1 - - + +
707B LYS* 1.3 77.4 + - + +
708B ASP 3.4 1.1 - - - -
710B GLU* 4.0 4.0 - - - +
1006B EDO 2.9 30.9 + - - -
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Residues in contact with LYS 707 (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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697B ASN* 5.7 0.4 - - - -
703B PHE* 3.0 46.3 + - + +
704B LEU* 3.1 5.1 + - - +
706B GLU* 1.3 94.6 + - - +
708B ASP* 1.3 65.3 + - - +
709B GLY 3.1 0.7 + - - -
710B GLU* 2.9 42.7 + - + +
711B PHE* 3.8 24.2 - - + -
813B TYR* 3.4 6.9 - - - -
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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