Contacts of the helix formed by residues 692 - 697 (chain B) in PDB entry 5M64
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 692 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690B GLU* 4.5 2.2 - - - -
691B PHE* 1.3 102.7 + - - +
693B PRO* 1.3 65.7 - - + +
694B THR* 3.0 34.8 + - + -
695B ASN* 3.0 25.1 + - - +
755B ASN* 6.2 2.2 - - - +
982B THR* 5.1 9.4 - - - +
983B PRO 5.4 2.7 - - - +
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Residues in contact with PRO 693 (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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992A PRO* 4.9 13.3 - - + +
525B TRP* 5.7 3.1 - - + -
676B VAL* 4.1 31.4 - - + +
677B THR* 5.0 10.3 - - + -
690B GLU* 4.9 3.6 - - + -
691B PHE 4.2 4.3 - - - +
692B THR* 1.3 86.9 - - + +
694B THR* 1.3 58.4 + - - +
695B ASN* 3.3 5.5 - - - +
696B ILE* 3.6 19.1 - - - +
983B PRO 5.1 0.7 - - - +
984B TRP* 3.6 43.5 + - + +
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Residues in contact with THR 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B HIS* 4.9 1.2 + - - +
692B THR* 3.0 25.3 + - + -
693B PRO* 1.3 76.4 - - - +
695B ASN* 1.3 61.6 + - - +
696B ILE 3.1 3.1 - - - -
697B LEU* 3.1 35.0 + - - +
702B ASN* 2.8 40.3 + - - +
755B ASN* 5.9 1.3 - - - +
756B LEU* 5.3 4.5 - - + -
982B THR* 5.7 3.4 - - - +
983B PRO* 3.3 29.1 - - + +
984B TRP* 4.1 5.2 - - - -
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Residues in contact with ASN 695 (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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546B ALA* 4.5 3.3 - - - +
547B HIS* 3.2 44.5 + - + +
548B LYS* 4.5 6.9 + - + +
651B ARG* 3.6 17.0 + - - +
652B PRO* 5.3 1.2 - - + +
690B GLU* 2.3 38.8 + - - +
691B PHE* 3.3 26.8 - - + -
692B THR 3.0 17.2 + - - +
693B PRO* 3.9 5.2 - - - +
694B THR* 1.3 79.9 - - + +
696B ILE* 1.3 69.2 + - - +
697B LEU 3.2 0.2 - - - -
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Residues in contact with ILE 696 (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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992A PRO* 6.3 1.1 - - + -
995A TYR* 6.3 2.5 - - + -
996A TYR* 4.0 15.9 - - + -
525B TRP* 3.6 43.5 - - + +
526B GLY* 3.5 37.0 - - - +
528B LEU 5.3 0.9 - - - +
529B CYS* 3.4 20.3 - - - -
530B PRO* 4.1 15.2 - - + +
546B ALA* 5.1 2.3 - - - +
651B ARG* 5.2 0.4 - - - +
693B PRO 3.6 17.3 - - - +
695B ASN* 1.3 82.4 + - - +
697B LEU* 1.3 80.8 + - + +
984B TRP* 5.6 0.9 - - + +
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Residues in contact with LEU 697 (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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995A TYR* 4.0 30.1 - - + +
529B CYS* 3.6 4.1 - - - -
530B PRO* 6.2 1.8 - - + -
531B VAL* 3.8 13.7 - - + -
547B HIS* 3.4 22.3 - - - +
694B THR* 3.1 38.8 + - - +
695B ASN 3.6 0.2 - - - +
696B ILE* 1.3 94.3 - - + +
698B SER* 1.3 62.8 + - - +
701B ALA* 3.7 21.8 - - + +
702B ASN* 3.7 19.7 - - + +
707B SER* 5.1 6.5 - - - -
708B ASP* 5.2 2.2 - - - +
983B PRO* 5.2 3.6 - - + -
984B TRP* 4.2 14.1 - - + +
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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