Contacts of the helix formed by residues 700 - 704 (chain B) in PDB entry 5M5X
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 LEU 700 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B TYR* 3.5 66.9 - - + +
497B ILE* 4.4 8.1 - - + -
498B SER* 4.0 2.7 - - - +
532B HIS* 3.4 37.7 - - + +
698B SER* 3.2 1.4 + - - -
699B ILE* 1.3 80.6 - - + +
701B ALA* 1.3 62.9 + - - +
703B LEU* 3.3 16.5 + - + +
704B THR 3.6 5.0 + - - -
718B GLN* 4.3 15.9 + - - +
719B CYS* 4.8 8.3 - - - +
722B GLY* 3.9 19.3 - - - -
723B LYS* 4.9 1.6 - - + -
920B ARG* 5.7 0.3 - - - -
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Residues in contact with ALA 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B VAL* 3.6 34.8 - - + -
532B HIS* 4.8 2.7 - - + -
697B LEU* 3.2 26.8 - - + +
698B SER* 3.0 16.4 + - - +
700B LEU* 1.3 72.2 - - - +
702B ASN* 1.3 59.9 + - - +
703B LEU 3.0 8.9 + - - -
704B THR* 3.1 26.1 - - + +
707B SER* 4.4 0.5 - - - -
718B GLN* 5.0 4.7 - - - +
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Residues in contact with ASN 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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547B HIS* 3.8 14.6 + - + -
694B THR* 3.0 45.1 + - - +
697B LEU* 3.5 10.5 - - + +
698B SER 2.8 21.0 + - - +
699B ILE* 4.4 2.7 - - - +
701B ALA* 1.3 75.1 - - - +
703B LEU* 1.3 57.1 + - - +
704B THR 4.7 2.7 - - - +
754B ALA* 3.4 19.4 - - - +
756B LEU* 3.3 38.6 - - + +
982B THR* 5.8 0.2 - - - -
983B PRO* 4.9 11.0 - - - +
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Residues in contact with LEU 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B TYR* 3.2 45.5 - - + +
699B ILE 3.4 18.1 + - - +
700B LEU* 3.5 9.4 - - + +
701B ALA 3.0 1.0 - - - -
702B ASN* 1.3 78.6 - - - +
704B THR* 1.3 64.0 + - - +
705B PRO* 3.7 1.7 - - - +
753B LYS* 5.5 1.2 - - - -
754B ALA* 4.5 13.8 + - - +
756B LEU 5.8 0.9 - - - +
757B TYR* 3.6 39.0 - - + +
762B MET* 4.3 13.0 - - + -
920B ARG* 3.4 31.8 + - - +
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Residues in contact with THR 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 3.6 2.2 + - - -
701B ALA* 3.1 20.8 + - - +
702B ASN 4.7 1.4 - - - +
703B LEU* 1.3 80.9 + - - +
705B PRO* 1.3 65.7 + - - +
706B PHE 3.6 2.3 + - - -
707B SER* 3.8 26.5 + - - +
710B ASN* 4.5 1.8 + - - +
715B ASN* 4.8 9.1 + - + +
718B GLN* 3.7 24.1 + - - +
920B ARG* 2.4 34.2 + - - +
921B HIS* 3.9 6.9 - - - -
981B SER* 4.1 5.2 + - - -
983B PRO* 4.6 5.7 - - - +
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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