Contacts of the strand formed by residues 764 - 773 (chain B) in PDB entry 3HS0
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 764 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A LEU 2.6 23.4 + - - -
231A TYR* 4.1 2.9 - - - -
232A GLY* 5.5 0.2 - - - -
559A ASP 3.9 0.3 - - - -
560A LYS* 2.9 54.2 + - + +
763B THR* 1.3 86.5 + - - +
765B TRP* 1.3 61.7 + - - +
785B GLU* 3.9 30.1 - - + +
786B ILE 3.2 11.9 - - - +
787B ARG* 3.6 20.6 - - + +
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Residues in contact with TRP 765 (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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557A ALA* 5.1 4.3 - - + -
558A VAL 3.7 2.9 - - - -
559A ASP* 3.5 38.1 - - + -
730B PRO* 3.5 27.4 - - + -
733B TRP* 3.1 40.5 - + + -
758B LEU* 3.7 25.9 - - + +
759B ARG* 4.1 14.2 + - + +
761B SER* 3.3 36.2 + - - -
763B THR* 3.7 7.7 - - + +
764B THR* 1.3 73.1 - - - +
766B VAL* 1.3 62.6 + - - +
767B VAL* 3.9 1.6 - - + -
784B TYR 3.7 0.9 - - - +
785B GLU* 3.2 5.7 - - - +
786B ILE* 2.8 49.4 + - + +
788B VAL* 3.5 33.7 - - + +
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Residues in contact with VAL 766 (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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556A VAL 3.8 0.5 - - - +
557A ALA* 3.6 0.9 - - - -
558A VAL* 2.8 42.2 + - + +
560A LYS* 4.1 21.8 - - + -
563A TYR* 3.8 37.7 - - + -
765B TRP* 1.3 75.8 - - - +
767B VAL* 1.3 62.0 + - - +
768B LEU* 3.7 26.2 + - + -
783B PRO* 3.9 16.2 - - + -
784B TYR 3.8 2.9 - - - +
785B GLU* 4.0 17.5 - - + +
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Residues in contact with VAL 767 (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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528A VAL* 4.6 21.1 - - + +
543A ILE* 4.8 10.5 - - + -
555A LEU* 5.1 8.5 - - + -
556A VAL 3.4 8.7 - - - +
557A ALA* 4.4 17.3 - - + -
734B LEU* 5.1 7.0 - - + -
756B PHE* 5.1 10.1 - - + -
765B TRP* 5.1 2.7 - - + +
766B VAL* 1.3 72.7 - - - +
768B LEU* 1.3 68.9 + - - +
769B ALA 4.1 1.0 + - - -
782B GLU 4.7 1.2 - - - +
783B PRO* 3.8 3.8 - - - +
784B TYR* 2.8 44.9 + - + +
786B ILE* 4.3 22.7 - - + -
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Residues in contact with LEU 768 (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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109A GLN* 5.0 9.6 + - - +
111A ASP 5.8 0.7 - - - +
554A GLY 3.6 1.4 - - - +
555A LEU* 3.5 4.2 - - - +
556A VAL* 3.0 50.8 + - + +
558A VAL* 4.2 9.6 - - + -
563A TYR* 3.5 39.9 - - + -
570A LYS* 4.1 17.0 - - + +
766B VAL* 3.8 15.9 - - + +
767B VAL* 1.3 76.3 - - - +
769B ALA* 1.3 61.0 + - - +
770B VAL* 5.3 2.9 - - + -
780B VAL* 6.5 2.2 - - + -
781B ALA 5.7 3.1 - - - +
782B GLU 6.2 0.2 - - - -
783B PRO* 4.0 17.9 - - + -
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Residues in contact with ALA 769 (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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526A LEU* 3.9 11.2 - - + -
528A VAL* 3.8 23.7 - - + +
545A LEU* 5.2 0.4 - - + -
553A VAL* 4.0 9.9 - - + -
554A GLY 3.3 4.3 - - - -
555A LEU* 3.7 21.1 - - + -
767B VAL 4.1 1.4 + - - -
768B LEU* 1.3 74.7 - - - +
770B VAL* 1.3 68.0 + - - +
780B VAL* 4.5 1.6 - - - +
781B ALA* 3.0 33.5 + - + +
782B GLU 6.0 0.4 + - - -
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Residues in contact with VAL 770 (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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109A GLN* 3.9 24.2 - - - +
126A PHE* 3.4 37.8 - - + -
526A LEU* 3.9 0.7 - - - -
552A ARG 3.9 1.2 - - - +
554A GLY* 2.7 40.0 + - - +
571A ILE* 4.8 9.9 - - + -
768B LEU* 5.3 2.7 - - + -
769B ALA* 1.3 81.7 - - - +
771B SER* 1.3 59.0 + - - +
778B ILE* 3.8 17.7 - - + -
779B CYS 3.3 9.4 - - - +
780B VAL* 4.1 22.0 - - + -
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Residues in contact with SER 771 (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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126A PHE* 4.9 1.6 - - - -
525A THR 4.4 3.8 + - - -
526A LEU* 3.3 26.4 - - - +
548A ASP* 5.4 1.2 + - - -
551A ALA* 4.4 11.2 - - - +
552A ARG 3.4 4.5 - - - -
553A VAL* 3.6 20.2 - - - +
770B VAL* 1.3 75.4 - - - +
772B PHE* 1.3 62.9 + - - +
773B THR* 4.9 2.9 - - - +
777B GLY 3.7 0.9 + - - +
778B ILE* 3.3 7.5 - - - +
779B CYS* 2.9 45.0 + - - +
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Residues in contact with PHE 772 (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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126A PHE* 4.5 16.6 - - + -
127A SER 3.4 26.2 - - - +
128A MET 4.2 12.1 - - - -
129A ASP* 4.3 0.9 - - - -
130A HIS* 3.3 35.9 - + + -
550A GLY 4.6 0.5 - - - +
551A ALA* 3.5 0.5 - - - -
552A ARG* 2.9 42.8 + - + +
771B SER* 1.3 74.7 - - - +
773B THR* 1.3 77.1 + - - +
774B PRO* 3.6 35.0 - - + -
777B GLY 3.5 11.0 - - - -
778B ILE* 4.7 2.0 - - + -
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Residues in contact with THR 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ASP* 3.9 21.5 - - + +
549A PRO 5.1 3.4 - - - +
550A GLY 5.1 1.3 - - - -
551A ALA* 3.4 32.8 - - + +
771B SER* 4.9 4.0 - - - +
772B PHE* 1.3 89.5 - - - +
774B PRO* 1.3 70.5 - - - +
775B THR* 3.7 3.6 + - - -
776B LYS* 3.0 30.0 + - + +
777B GLY 3.0 26.0 + - - +
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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