Contacts of the strand formed by residues 715 - 720 (chain B) in PDB entry 2WAC
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 715 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710B ILE* 3.7 2.6 - - - +
711B THR* 2.5 45.6 + - - +
713B THR* 3.5 17.0 + - - +
714B LEU* 1.3 83.4 - - - +
716B PHE* 1.3 61.9 + - - +
813B GLU* 2.7 29.5 + - - +
814B TYR 3.3 15.7 - - - +
815B ALA* 4.4 14.8 - - + +
856B PRO* 4.9 6.7 - - + -
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Residues in contact with PHE 716 (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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707B VAL* 4.1 23.6 - - + -
709B GLU 3.2 12.1 - - - +
710B ILE* 4.1 8.5 - - + +
711B THR 4.6 0.4 - - - +
714B LEU 4.4 1.1 - - - -
715B THR* 1.3 79.5 - - - +
717B PHE* 1.3 70.9 + - - +
718B ALA* 4.3 4.3 - - + -
812B THR 3.6 0.5 - - - +
813B GLU* 3.3 1.2 - - - -
814B TYR* 2.8 72.7 + + + -
815B ALA 4.2 0.7 - - - -
816B LEU* 4.1 25.6 - - + -
835B PHE* 4.2 17.7 - + + -
846B LEU* 4.0 8.1 - - + -
859B ALA* 4.5 6.5 - - + -
861B LEU* 3.6 40.6 - - + -
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Residues in contact with PHE 717 (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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707B VAL* 3.5 5.9 - - - +
708B THR* 2.9 25.3 + - - +
709B GLU* 2.8 22.7 + - + +
711B THR* 4.2 13.5 - - + -
716B PHE* 1.3 77.7 - - - +
718B ALA* 1.3 59.6 + - - +
782B LEU* 4.3 20.4 - - + -
784B ILE* 5.7 2.2 - - - -
786B TYR 3.7 17.3 - - - +
787B GLY* 3.6 32.8 - - - -
789B LYS* 5.8 3.6 - - - -
811B ALA* 4.2 15.9 - - + -
812B THR 3.3 7.0 - - - -
813B GLU* 3.7 51.4 - - + -
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Residues in contact with ALA 718 (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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705B VAL* 3.9 26.7 - - + -
706B ILE 3.3 12.3 - - - +
707B VAL* 4.4 1.3 - - - -
708B THR* 4.3 0.7 - - - -
716B PHE* 4.3 17.5 - - + -
717B PHE* 1.3 76.6 - - - +
719B GLN* 1.3 62.5 + - - +
720B SER 4.4 0.2 + - - -
810B TYR 3.8 0.9 - - - +
811B ALA* 3.4 2.9 - - - -
812B THR* 2.9 34.0 + - - +
814B TYR* 4.4 4.0 - - + -
846B LEU* 4.4 7.0 - - + -
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Residues in contact with GLN 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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705B VAL* 3.0 8.5 - - - +
706B ILE* 2.8 45.4 + - + +
708B THR* 3.5 24.5 - - + +
718B ALA* 1.3 75.6 - - - +
720B SER* 1.3 65.9 + - - +
724B GLY* 5.8 3.2 - - - -
727B LEU* 3.5 21.5 - - + +
785B ASP 2.8 26.7 + - - +
786B TYR* 3.5 23.2 - - - -
810B TYR* 3.4 20.2 - - + +
811B ALA* 4.3 0.9 - - + -
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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
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703B GLU* 5.2 8.9 + - - +
704B ASN 3.8 9.8 + - - -
705B VAL* 4.3 6.6 - - - +
706B ILE* 6.0 0.7 - - - -
718B ALA 4.4 0.2 + - - -
719B GLN* 1.3 76.8 - - - +
721B VAL* 1.3 67.0 + - - +
722B GLU* 4.3 7.4 + - - +
723B SER* 3.2 30.4 + - - -
724B GLY* 3.5 8.0 + - - -
810B TYR 4.2 3.8 + - - -
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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