Contacts of the strand formed by residues 720 - 727 (chain B) in PDB entry 2B5L
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 SER 720 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B ALA* 3.8 6.9 - - - +
382B PHE* 2.9 36.0 + - - +
719B GLU* 1.3 70.1 - - - +
721B PRO* 1.3 66.8 - - - +
722B ARG* 4.1 21.1 + - - +
737B SER* 3.0 7.9 - - - -
738B SER* 2.8 49.5 + - - -
740B ILE* 5.4 1.7 - - - +
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Residues in contact with PRO 721 (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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360B VAL* 3.3 13.8 - - - +
378B CYS* 3.7 25.1 - - + -
379B SER 3.6 9.0 - - - +
380B GLY 4.5 3.3 - - - +
381B ALA* 4.5 6.3 - - - -
385B GLY* 3.7 8.3 - - - -
386B SER 3.4 32.8 - - - +
387B LEU* 4.7 0.2 - - + -
717B LEU* 3.6 18.4 - - + -
719B GLU 3.4 4.0 - - - +
720B SER* 1.3 85.9 - - - +
722B ARG* 1.3 67.3 + - - +
735B VAL* 4.6 4.7 - - + -
736B LEU 3.8 4.7 - - - +
737B SER* 4.5 1.8 - - - -
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Residues in contact with ARG 722 (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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360B VAL* 3.2 33.1 - - + +
361B ASP* 3.5 9.0 - - - +
378B CYS* 4.4 1.1 - - - -
720B SER* 4.1 19.5 - - - +
721B PRO* 1.3 83.1 - - - +
723B LYS* 1.3 73.4 + - + +
736B LEU* 2.7 27.3 + - + +
737B SER 5.0 0.4 - - - -
738B SER* 3.8 13.6 + - - -
787B GLU* 3.1 31.1 + - - -
789B HIS* 4.0 16.5 - - + +
812B TYR* 5.4 0.8 - - - -
813B ALA 4.7 11.9 + - - +
814B LEU* 5.4 0.2 - - - +
28D THR* 3.1 43.4 + - - +
31D GLN* 6.0 0.7 - - - +
32D VAL* 5.7 7.8 - - - +
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Residues in contact with LYS 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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360B VAL* 5.2 2.6 + - - +
361B ASP* 3.1 27.6 + - - +
378B CYS* 3.5 1.6 - - - -
722B ARG* 1.3 89.5 + - + +
724B ILE* 1.3 64.4 + - - +
734B GLY 4.2 0.4 - - - -
735B VAL* 3.1 11.4 - - - +
736B LEU* 3.0 48.6 + - + -
814B LEU 3.5 28.0 + - - +
815B SER* 4.6 4.5 - - - +
816B LEU* 4.0 18.2 - - + +
871B TYR 5.4 3.5 + - - -
27D PHE* 5.4 6.9 - - - -
31D GLN* 5.0 13.3 + - - +
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Residues in contact with ILE 724 (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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361B ASP* 3.1 24.5 + - + +
362B MET* 4.0 19.2 - - - +
363B CYS* 4.3 9.4 - - - +
376B VAL* 4.0 23.8 - - + +
378B CYS* 3.3 17.7 - - - -
387B LEU* 4.3 13.5 - - + -
723B LYS* 1.3 80.2 - - - +
725B CYS* 1.3 68.2 + - - +
733B PHE* 3.4 31.6 - - + -
734B GLY 3.0 12.3 - - - +
735B VAL* 3.8 14.1 - - + -
816B LEU* 4.1 2.8 - - - +
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Residues in contact with CYS 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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363B CYS* 4.7 7.0 - - - -
724B ILE* 1.3 80.6 - - - +
726B TYR* 1.3 59.2 + - - +
733B PHE* 3.3 4.3 - - - +
734B GLY 2.8 29.3 + - - -
816B LEU* 3.5 37.2 - - + +
817B VAL* 4.1 0.9 - - - -
818B SER* 3.8 34.5 - - - +
829B PHE* 4.0 10.5 - - - -
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Residues in contact with TYR 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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363B CYS* 4.7 4.2 - - - +
365B VAL* 3.7 40.4 - - + +
725B CYS* 1.3 75.0 - - - +
727B GLN* 1.3 59.5 + - - +
728B GLU* 3.7 31.4 + - + +
731B GLN* 3.9 9.7 + - - -
732B CYS 3.2 19.1 - - - -
733B PHE* 3.3 30.3 - + + +
796B GLN* 2.7 39.5 + - - -
818B SER* 3.9 10.4 + - - -
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Residues in contact with GLN 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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725B CYS 4.1 1.2 + - - -
726B TYR* 1.3 72.3 - - - +
728B GLU* 1.3 66.6 + - - +
729B VAL* 4.1 3.6 - - + -
730B SER* 2.6 28.9 + - - +
731B GLN 3.2 13.3 + - - -
732B CYS 2.8 18.8 + - - +
818B SER* 3.2 14.6 + - - +
827B THR* 3.5 29.6 + - + +
828B TYR 3.3 28.9 + - - -
829B PHE* 3.0 48.1 - - + -
853B TYR* 4.0 8.5 - - - +
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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