Contacts of the strand formed by residues 785 - 795 (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 GLU 785 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277B GLU* 4.4 13.2 - - - +
740B ILE* 3.7 27.8 - - + +
741B GLU 3.2 4.7 - - - -
742B VAL* 4.8 12.7 - - + +
752B LEU* 5.3 4.0 - - - +
783B GLY 5.9 0.2 - - - +
784B GLU* 1.3 79.9 - - - +
786B VAL* 1.3 72.1 + - - +
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Residues in contact with VAL 786 (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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740B ILE* 4.6 2.2 - - - -
741B GLU* 2.7 45.8 + - + +
742B VAL 5.4 2.9 - - - -
743B GLN* 4.4 24.9 - - + +
748B GLY 5.4 6.1 - - - +
749B THR* 5.9 2.7 - - + -
784B GLU* 4.9 0.9 - - + -
785B GLU* 1.3 82.4 - - - +
787B GLU* 1.3 66.5 + - - +
788B VAL* 3.6 12.5 + - + +
810B ASN* 5.7 6.1 - - - +
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Residues in contact with GLU 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B ARG* 3.1 18.0 + - - -
738B SER* 2.5 26.5 + - - +
739B ARG 3.4 6.3 - - - +
740B ILE* 4.7 10.8 - - + +
786B VAL* 1.3 77.4 - - - +
788B VAL* 1.3 61.9 + - - +
789B HIS* 2.8 19.2 + - - +
810B ASN* 5.1 9.9 + - - -
811B GLU 5.6 1.2 + - - +
812B TYR* 3.5 43.0 + - + +
25D GLU* 4.5 5.5 - - - +
28D THR* 5.0 2.8 + - - -
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Residues in contact with VAL 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B SER 4.0 0.5 - - - +
738B SER* 3.5 1.0 - - - -
739B ARG* 2.9 49.2 + - + +
741B GLU* 4.1 24.2 - - + +
749B THR* 5.3 4.5 - - + -
786B VAL* 3.7 17.3 - - + +
787B GLU* 1.3 81.3 - - - +
789B HIS* 1.3 64.6 + - - +
790B ASN* 4.2 2.3 + - - -
806B GLN* 3.8 37.5 - - + +
807B PHE 5.0 3.8 - - - +
811B GLU 5.6 0.2 - - - -
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Residues in contact with HIS 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B ARG* 4.0 17.4 - - + +
736B LEU* 6.5 0.2 - - + -
737B SER 3.2 9.4 - - - +
738B SER* 3.0 19.3 + - - -
787B GLU* 2.8 30.0 + - + +
788B VAL* 1.3 82.2 - - - +
790B ASN* 1.3 69.9 + - - +
806B GLN* 3.8 3.8 - - - +
807B PHE* 3.1 26.4 + - + +
811B GLU 3.7 18.8 + - - +
812B TYR* 3.1 34.5 - + + -
813B ALA* 3.0 36.1 + - + +
814B LEU* 5.7 0.2 - - + -
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Residues in contact with ASN 790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B GLU* 4.6 0.8 + - - -
736B LEU* 3.6 3.7 - - - +
737B SER* 3.1 58.4 + - - -
738B SER* 5.0 0.2 - - - +
739B ARG* 3.3 31.2 + - - -
757B SER* 3.5 15.7 - - - +
788B VAL* 4.2 3.6 + - - +
789B HIS* 1.3 83.8 - - - +
791B LEU* 1.3 60.6 + - - +
792B LEU* 4.3 2.0 - - + +
804B ALA* 4.7 3.2 - - - +
805B HIS 2.7 23.6 - - - +
806B GLN* 3.4 10.9 - - - +
807B PHE* 3.4 12.0 - - - -
813B ALA* 5.4 0.4 - - - +
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Residues in contact with LEU 791 (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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734B GLY* 4.1 5.6 - - - -
735B VAL 3.5 18.6 - - - +
736B LEU* 3.5 25.4 - - + -
790B ASN* 1.3 73.0 - - - +
792B LEU* 1.3 69.3 + - - +
793B ILE* 4.2 3.1 + - + -
803B HIS 3.8 1.2 - - - +
804B ALA* 3.6 3.1 - - - -
805B HIS* 2.9 35.1 + - + +
807B PHE* 3.5 11.0 - - + -
816B LEU* 3.9 11.9 - - + -
829B PHE* 4.2 18.4 - - + -
831B VAL* 4.0 17.0 - - + -
851B PHE* 4.1 19.5 - - + -
858B LEU* 4.4 18.3 - - + +
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Residues in contact with LEU 792 (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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717B LEU* 5.0 7.2 - - + -
719B GLU* 3.7 11.0 - - + +
733B PHE 3.5 0.7 - - - +
734B GLY* 3.4 5.7 - - - -
735B VAL* 2.7 48.8 + - + +
737B SER* 3.1 32.8 - - - +
756B ALA* 4.0 18.2 - - + -
757B SER* 3.8 14.8 - - - +
790B ASN* 4.3 4.7 - - - +
791B LEU* 1.3 79.7 - - - +
793B ILE* 1.3 63.2 + - - +
794B ILE* 4.0 15.4 + - + -
801B VAL* 4.2 4.9 - - + -
803B HIS 3.5 4.5 - - - +
804B ALA* 3.8 25.4 - - + -
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Residues in contact with ILE 793 (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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732B CYS* 3.7 25.1 - - + -
733B PHE 3.4 3.8 - - - +
734B GLY* 5.2 0.9 - - - -
791B LEU* 5.1 4.7 - - + +
792B LEU* 1.3 77.8 - - - +
794B ILE* 1.3 62.0 + - - +
802B LEU* 2.8 32.4 + - + +
803B HIS* 3.2 20.9 + - + +
829B PHE* 3.5 38.6 - - + -
853B TYR* 3.8 39.5 - - + +
858B LEU* 4.1 22.4 - - + -
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Residues in contact with ILE 794 (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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387B LEU* 4.3 20.6 - - + -
715B VAL* 5.8 0.4 - - + -
717B LEU* 5.3 5.6 - - + -
732B CYS* 2.9 7.1 - - - +
733B PHE* 2.9 40.3 + - + +
735B VAL* 4.5 15.7 - - + -
792B LEU* 4.1 13.0 - - + +
793B ILE* 1.3 81.0 - - - +
795B ASP* 1.3 65.5 + - - +
799B PHE* 3.4 45.5 - - + +
800B GLU 4.0 1.3 - - - -
801B VAL* 3.5 37.2 - - + -
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Residues in contact with ASP 795 (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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730B SER 5.4 0.5 - - - +
731B GLN* 3.9 13.6 - - - +
732B CYS* 4.2 2.5 - - - -
793B ILE 4.2 0.2 + - - -
794B ILE* 1.3 74.9 - - - +
796B GLN* 1.3 61.7 + - - +
797B HIS* 3.1 21.0 + - - +
798B THR* 2.8 50.2 + - - +
799B PHE* 2.6 32.2 + - - -
800B GLU 3.5 8.2 + - - +
802B LEU* 4.2 22.9 - - + +
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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