Contacts of the strand formed by residues 734 - 740 (chain B) in PDB entry 1B0P
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 TYR 734 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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708B LEU* 3.6 32.8 - - + -
709B ALA 3.6 5.6 - - - -
710B LYS* 3.7 44.0 + - + +
725B GLU* 3.9 2.1 - - - +
726B ALA* 3.0 24.7 + - + +
730B GLU 4.2 7.6 - - - -
731B LEU* 3.8 20.8 + - + -
732B LYS 3.3 5.5 - - - +
733B GLY* 1.3 84.0 - - - +
735B LYS* 1.3 67.0 + - - +
787B LYS* 4.0 17.9 - - + +
790B VAL* 3.9 29.3 - - + +
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Residues in contact with LYS 735 (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 1.4 - - - +
708B LEU* 3.2 8.7 - - - +
709B ALA* 2.7 39.3 + - + +
711B GLU* 4.1 31.2 - - + +
714B LEU* 4.0 18.4 - - + -
723B ALA* 3.6 34.2 + - + -
724B LEU 3.2 8.7 - - - +
725B GLU* 4.1 16.5 - - + +
733B GLY 4.6 2.9 - - - +
734B TYR* 1.3 85.9 - - - +
736B PHE* 1.3 59.1 + - - +
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Residues in contact with PHE 736 (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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684B TRP* 3.6 8.7 - + - -
689B CYS* 4.1 4.5 - - - -
691B GLN* 3.4 64.2 - - + +
693B ASN* 3.2 32.5 - - - -
706B PRO* 4.7 2.5 - - + -
707B VAL 3.3 10.3 - - - -
708B LEU* 4.3 4.7 - - + -
723B ALA* 3.4 2.1 - - - -
724B LEU* 2.7 40.9 + - + +
726B ALA* 4.3 5.8 - - + +
731B LEU* 5.8 0.4 - - + -
735B LYS* 1.3 73.0 - - - +
737B ARG* 1.3 62.7 + - - +
738B ILE* 3.6 31.4 - - + -
797B LYS* 5.0 1.6 - - - -
801B PHE* 3.8 27.8 - + - -
1233B SF4 4.5 0.4 - - - -
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Residues in contact with ARG 737 (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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684B TRP* 3.6 22.9 - - + +
686B PRO* 5.3 1.2 - - - +
705B LEU 3.5 1.4 - - - +
706B PRO 3.6 0.2 - - - -
707B VAL* 2.7 44.8 + - + +
720B ASN 3.5 19.0 + - - -
721B PHE* 3.8 28.9 - - + -
722B THR* 2.7 41.3 + - - +
723B ALA* 4.0 7.4 - - + -
736B PHE* 1.3 79.7 - - - +
738B ILE* 1.3 72.6 + - - +
739B GLN* 2.4 49.7 - - + +
774B GLN* 3.4 18.0 + - - +
777B ASN* 4.3 2.8 + - - -
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Residues in contact with ILE 738 (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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684B TRP* 3.6 51.1 - - + +
693B ASN* 4.0 11.0 - - - +
695B CYS* 3.5 30.1 - - - -
704B ILE* 3.8 23.8 - - + -
705B LEU 3.9 0.2 - - - -
706B PRO* 4.2 10.5 - - + -
736B PHE* 3.6 32.1 - - + -
737B ARG* 1.3 80.9 + - - +
739B GLN* 1.3 60.7 + - - +
740B ILE* 3.9 17.2 + - + +
762B LEU* 4.6 2.7 - - + -
1233B SF4 4.1 5.6 - - - -
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Residues in contact with GLN 739 (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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704B ILE* 3.6 1.3 - - - -
705B LEU* 2.8 50.9 + - + +
707B VAL* 4.2 13.5 - - + -
721B PHE* 3.4 12.5 - - - -
737B ARG* 2.4 31.6 + - + +
738B ILE* 1.3 72.0 - - - +
740B ILE* 1.3 83.6 + - - +
741B ASN* 3.6 0.7 + - - -
774B GLN* 2.5 26.2 + - - +
777B ASN* 3.3 22.8 - - - +
778B LEU* 3.9 24.9 - - + +
781B ALA* 4.1 6.1 - - + -
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Residues in contact with ILE 740 (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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681B VAL* 4.9 1.1 - - + -
682B PRO* 3.6 52.3 - - + +
683B GLN* 4.8 0.4 - - - -
684B TRP* 4.6 9.6 - - + +
703B ALA 3.7 5.8 - - - +
704B ILE* 4.1 12.3 - - + -
738B ILE* 3.9 25.0 + - + +
739B GLN* 1.3 99.6 + - - +
741B ASN* 1.3 62.2 + - - +
742B THR* 3.3 25.4 + - + +
745B CYS* 4.9 0.9 - - + -
762B LEU* 4.2 9.6 - - + -
774B GLN* 4.2 13.6 - - + +
778B LEU* 4.1 5.9 - - - +
1234B SF4 4.9 3.6 - - - -
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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