Contacts of the helix formed by residues 718 - 727 (chain B) in PDB entry 5YWB
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 718 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695B THR* 5.2 8.0 + - - -
699B ILE* 5.7 0.2 - - - +
716B GLY 3.7 2.4 - - - -
717B CYS* 1.3 78.1 - - - +
719B LYS* 1.3 59.5 + - - +
721B SER* 3.7 18.2 - - - -
722B LEU* 2.9 30.0 + - - +
903B MET* 4.5 7.0 - - - +
906B GLY* 4.9 3.1 - - - +
2501B ADP 3.2 15.5 + - - -
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Residues in contact with LYS 719 (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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711B ILE* 3.9 18.7 - - + +
712B VAL* 4.0 20.6 - - - -
713B GLY* 3.4 24.0 + - - +
714B GLN 4.0 3.4 - - - -
717B CYS* 4.2 10.8 - - + +
718B GLY* 1.3 72.8 - - - +
720B SER* 1.3 61.5 + - - +
721B SER 3.1 0.7 - - - -
722B LEU* 3.3 5.7 + - - +
723B LEU* 2.9 30.7 + - - +
854B ASP* 5.2 0.2 - - - -
887B VAL* 3.6 32.4 - - + +
888B THR* 4.6 6.5 + - - +
889B HIS* 4.5 12.7 + - - -
903B MET* 4.4 7.0 - - + -
1513B ASP* 4.1 8.7 + - - -
2501B ADP 2.6 39.8 + - - +
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Residues in contact with SER 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B LYS* 1.3 77.3 - - - +
721B SER* 1.3 57.0 + - - +
723B LEU* 3.2 5.8 + - - +
724B LEU* 2.9 38.1 + - - +
775B GLN* 2.9 8.2 + - - -
854B ASP* 3.0 27.8 + - - -
2501B ADP 3.2 13.5 + - - -
2503B MG 2.4 30.2 - - - -
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Residues in contact with SER 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B TRP* 3.7 21.3 - - - -
695B THR* 5.7 4.9 - - - -
696B LEU* 6.1 3.8 - - - -
718B GLY* 3.7 13.6 - - - -
719B LYS 3.1 0.6 - - - -
720B SER* 1.3 75.5 - - - +
722B LEU* 1.3 60.6 + - - +
724B LEU* 3.2 4.6 + - - +
725B ALA* 2.9 31.5 + - - +
730B MET* 4.3 6.4 - - - +
2501B ADP 3.5 39.1 + - - -
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Residues in contact with LEU 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B ILE* 4.2 12.6 - - + -
696B LEU* 6.0 4.7 - - + +
699B ILE* 4.3 29.2 - - + -
701B ILE* 4.9 13.2 - - + -
711B ILE* 4.0 29.2 - - + -
718B GLY 2.9 20.2 + - - +
719B LYS 3.6 4.3 - - - +
721B SER* 1.3 75.7 - - - +
723B LEU* 1.3 51.1 + - - +
725B ALA* 4.6 5.2 - - + -
726B THR* 2.7 60.2 + - + +
732B LYS* 5.6 2.0 - - - +
901B ILE* 4.9 7.2 - - + -
903B MET* 4.4 21.5 - - - -
908B ILE* 5.8 1.1 - - + -
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Residues in contact with LEU 723 (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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711B ILE* 4.3 5.8 - - + -
719B LYS 2.9 11.1 + - - +
720B SER* 3.3 10.5 - - - +
721B SER 3.2 0.2 - - - -
722B LEU* 1.3 77.6 - - - +
724B LEU* 1.3 59.8 + - + +
726B THR* 2.5 17.6 + - - -
727B LEU* 3.2 18.7 + - - +
772B TYR* 3.6 27.4 - - + -
852B PHE* 3.5 39.3 - - + -
853B LEU 4.5 1.6 - - - -
854B ASP* 3.7 30.3 - - + +
885B VAL* 4.2 8.7 - - + +
887B VAL* 3.7 26.2 - - + -
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Residues in contact with LEU 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B THR* 5.8 2.2 - - + +
688B TRP* 4.5 16.8 - - + -
720B SER* 2.9 24.4 + - - +
721B SER* 3.2 4.9 + - - +
723B LEU* 1.3 76.3 - - - +
725B ALA* 1.3 65.7 + - - +
727B LEU* 3.0 30.5 + - + +
729B GLU* 3.4 22.0 + - + +
730B MET* 3.8 7.8 + - + -
772B TYR* 3.4 34.3 - - + +
854B ASP* 5.5 0.4 - - - +
1212B THR* 4.3 23.1 - - + -
1480B GLU* 4.3 17.0 - - - +
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Residues in contact with ALA 725 (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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696B LEU* 4.1 10.3 - - + -
721B SER 2.9 16.7 + - - +
722B LEU* 4.0 5.6 - - + +
724B LEU* 1.3 72.7 - - - +
726B THR* 1.3 65.2 + - + +
727B LEU 3.0 1.6 - - - -
728B GLY* 2.9 15.4 + - - -
730B MET* 3.7 35.8 - - + +
732B LYS* 3.9 24.9 - - - -
737B VAL* 4.9 5.0 - - - +
739B TRP* 4.8 2.3 - - - -
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Residues in contact with THR 726 (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 VAL* 4.9 12.5 - - + +
681B ILE* 3.5 32.0 - - + +
701B ILE* 5.5 1.1 - - + -
703B ILE* 5.5 6.1 - - + -
722B LEU* 2.7 28.9 + - + +
723B LEU* 2.5 28.1 + - - -
725B ALA* 1.3 73.8 - - - +
727B LEU* 1.3 55.0 + - - +
728B GLY 3.1 0.4 - - - -
737B VAL* 4.8 2.2 - - - -
739B TRP* 3.0 31.5 - - - -
852B PHE* 3.9 24.9 - - + -
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Residues in contact with LEU 727 (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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723B LEU 3.2 10.1 + - - +
724B LEU* 3.0 30.5 + - + +
725B ALA 3.0 1.0 - - - -
726B THR* 1.3 75.7 + - - +
728B GLY* 1.3 55.6 + - - +
729B GLU* 3.0 16.0 + - + +
739B TRP* 4.2 4.0 - - - -
770B VAL* 3.7 30.2 - - + +
772B TYR* 3.9 22.2 - - + -
852B PHE* 3.8 26.5 - - + -
1212B THR* 4.5 5.4 - - - +
1215B ARG 5.3 3.8 - - - +
1216B ALA* 3.6 27.9 - - + -
1218B ARG* 4.1 14.7 + - - -
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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