Contacts of the helix formed by residues 706 - 718 (chain B) in PDB entry 1B70
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 PRO 706 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704B PRO 3.3 4.0 - - - +
705B THR* 1.3 96.2 - - + +
707B TYR* 1.3 68.1 + - - +
708B GLY* 3.1 5.6 + - - +
709B GLU* 3.4 33.6 + - + +
710B VAL* 2.9 16.8 - - - +
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Residues in contact with TYR 707 (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 THR 3.9 1.6 + - - -
706B PRO* 1.3 69.4 - - - +
708B GLY* 1.3 73.4 + - - +
710B VAL* 2.9 23.7 + - + +
711B GLU* 3.0 41.9 - - + +
725B LEU* 4.6 2.9 + - - +
726B ALA* 4.9 0.9 - - - -
727B LEU* 3.4 51.8 + - + +
730B LEU* 5.8 4.3 - - + -
741B LYS* 5.6 1.0 - - - +
743B LEU* 5.8 5.8 - - + -
745B PHE* 4.0 13.9 - + - -
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Residues in contact with GLY 708 (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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626B VAL 6.1 1.3 - - - -
706B PRO* 3.0 6.9 - - - +
707B TYR* 1.3 88.5 - - - +
709B GLU* 1.3 61.8 + - - -
710B VAL 2.7 0.3 + - - -
711B GLU* 2.8 13.2 + - - +
712B ALA* 2.8 13.5 + - - -
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Residues in contact with GLU 709 (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 THR* 4.2 7.7 - - + +
706B PRO* 3.4 36.7 + - + +
708B GLY* 1.3 69.7 - - - +
710B VAL* 1.3 54.0 + - - +
712B ALA* 3.1 10.9 - - + +
713B LEU* 2.7 37.1 + - - +
775B ARG* 5.6 7.7 + - - +
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Residues in contact with VAL 710 (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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699B VAL* 4.7 14.6 - - + -
701B VAL* 4.8 11.7 - - + -
705B THR* 4.0 16.4 - - + +
706B PRO 2.9 23.1 - - - +
707B TYR* 2.9 11.7 - - + +
708B GLY 2.7 3.8 + - - -
709B GLU* 1.3 74.8 - - - +
711B GLU* 1.3 66.4 + - - +
713B LEU* 3.0 7.6 + - - +
714B VAL* 2.7 30.3 + - + +
741B LYS* 6.5 0.4 - - - -
743B LEU* 3.4 32.1 - - + -
745B PHE* 4.5 1.8 - - + -
772B LEU* 6.0 1.3 - - + -
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Residues in contact with GLU 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707B TYR* 3.0 42.6 + - + +
708B GLY* 2.8 10.3 + - - +
710B VAL* 1.3 75.7 - - - +
712B ALA* 1.3 55.9 + - - +
714B VAL* 3.4 6.0 + - - +
715B ARG* 2.7 79.5 + - - +
725B LEU* 3.7 22.6 - - + +
745B PHE* 4.3 4.5 - - + -
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Residues in contact with ALA 712 (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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708B GLY 2.8 13.3 + - - +
709B GLU* 3.1 18.4 - - + +
711B GLU* 1.3 80.6 + - - +
713B LEU* 1.3 58.2 + - - +
715B ARG* 3.5 4.9 - - - +
716B GLU* 2.8 32.8 + - - +
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Residues in contact with LEU 713 (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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709B GLU 2.7 19.3 + - - +
710B VAL* 3.7 4.0 - - - +
712B ALA* 1.3 70.4 - - - +
714B VAL* 1.3 71.0 + - + +
716B GLU* 2.9 25.0 + - + +
717B ALA* 3.0 23.4 + - + +
768B VAL* 6.2 0.2 - - + -
771B ALA* 3.8 29.6 - - + +
772B LEU* 3.8 16.2 - - + +
775B ARG* 3.6 36.1 - - + +
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Residues in contact with VAL 714 (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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697B LEU* 5.3 9.0 - - + -
699B VAL* 4.8 7.0 - - + -
710B VAL* 2.7 32.1 - - + +
711B GLU* 3.7 1.8 - - - +
713B LEU* 1.3 73.1 - - - +
715B ARG* 1.3 57.6 + - - +
717B ALA* 3.3 1.2 + - - -
718B ALA* 2.9 30.2 + - + +
725B LEU* 4.8 5.6 - - + -
745B PHE* 3.8 32.8 - - + -
747B LEU* 5.5 11.2 - - + -
768B VAL* 3.9 25.5 - - + +
772B LEU* 4.5 17.4 - - + +
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Residues in contact with ARG 715 (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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711B GLU* 2.7 55.4 + - - +
712B ALA* 3.5 4.5 - - - +
714B VAL* 1.3 73.9 - - - +
716B GLU* 1.3 64.3 + - + +
717B ALA 3.0 1.6 + - - -
718B ALA* 3.2 19.0 + - - +
719B GLY 4.5 3.3 + - - +
722B LEU* 4.1 20.7 + - + +
723B GLU 4.7 11.1 + - - -
724B SER* 5.5 0.2 - - - +
725B LEU* 3.4 40.8 + - + +
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Residues in contact with GLU 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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712B ALA 2.8 21.3 + - - +
713B LEU* 2.9 13.2 + - + +
715B ARG* 1.3 73.1 - - - +
717B ALA* 1.3 58.8 + - - +
719B GLY* 4.9 1.7 + - - -
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Residues in contact with ALA 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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713B LEU* 3.0 24.1 + - + +
714B VAL 3.9 0.2 - - - +
716B GLU* 1.3 76.9 - - - +
718B ALA* 1.3 66.6 + - - +
719B GLY* 2.9 7.3 + - - -
767B ARG* 4.1 18.3 - - - +
768B VAL* 3.1 36.4 - - + +
771B ALA* 5.4 3.8 - - + -
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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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714B VAL* 2.9 12.3 + - + +
715B ARG* 3.2 9.1 + - - +
717B ALA* 1.3 75.8 - - - +
719B GLY* 1.3 57.4 + - - +
722B LEU* 3.5 42.4 - - + -
747B LEU* 5.2 4.9 - - + -
749B PHE* 3.5 25.0 - - + -
764B ALA* 4.0 16.2 - - - +
768B VAL* 3.4 12.8 - - + -
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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