Contacts of the helix formed by residues 605 - 621 (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 GLY 605 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589B LEU* 3.8 5.1 - - - +
591B GLY 5.5 0.4 + - - -
604B SER* 1.3 83.1 + - - +
606B TYR* 1.3 56.8 + - - +
607B PHE 3.3 0.7 - - - -
608B LEU* 2.8 31.3 + - - +
609B LEU 3.4 2.6 + - - -
669B HIS* 3.5 22.4 - - - -
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Residues in contact with TYR 606 (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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605B GLY* 1.3 71.3 - - - -
607B PHE* 1.3 103.1 + + + +
608B LEU 2.9 5.4 + - - -
609B LEU* 3.0 7.4 + - - +
610B LYS* 2.9 30.4 + - + +
626B VAL* 3.4 29.3 - - - +
638B VAL* 4.4 23.8 - - + -
639B SER 6.1 1.3 - - - -
640B GLY* 6.4 0.2 - - - -
652B LEU* 3.9 32.6 - - + +
653B GLY* 4.3 20.6 - - - -
669B HIS* 3.2 29.4 - - + -
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Residues in contact with PHE 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU* 6.0 0.4 - - - -
604B SER 4.3 3.8 + - - +
605B GLY 3.2 1.2 + - - -
606B TYR* 1.3 110.1 - + + +
608B LEU* 1.3 57.0 + - - +
610B LYS* 3.9 21.8 - - + +
611B GLY* 3.1 19.1 + - - -
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Residues in contact with LEU 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 4.8 7.9 - - + -
589B LEU* 3.5 26.9 - - + -
593B GLY* 4.2 7.9 - - - -
594B VAL* 4.2 10.5 - - + +
603B LEU* 3.6 30.1 - - + +
604B SER* 3.5 33.0 + - - +
605B GLY 2.8 13.9 + - - +
607B PHE* 1.3 76.2 - - - +
609B LEU* 1.3 65.7 + - - +
611B GLY* 2.7 14.4 + - - -
612B TYR* 3.0 36.8 + - + -
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Residues in contact with LEU 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B PHE* 6.2 1.8 - - + -
569B LEU* 5.1 5.8 - - + -
588B LEU 4.4 2.2 - - - -
589B LEU* 3.2 39.9 - - + +
605B GLY 3.4 2.4 + - - +
606B TYR* 3.0 10.2 + - - +
608B LEU* 1.3 81.3 - - - +
610B LYS* 1.3 62.5 + - - +
612B TYR* 3.2 8.5 + - + +
613B LEU* 2.9 45.3 + - + +
652B LEU* 3.0 35.2 - - + -
669B HIS* 3.4 28.7 - - + +
670B LEU 3.8 0.7 - - - +
671B PHE* 3.5 20.9 - - + -
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Residues in contact with LYS 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B TYR* 2.9 26.3 + - + +
607B PHE* 4.1 27.6 - - + +
609B LEU* 1.3 76.1 - - - +
611B GLY* 1.3 65.7 + - - +
613B LEU* 2.9 9.1 + - - +
614B GLU* 2.8 59.4 + - + +
624B PHE* 4.2 6.9 - - + -
625B ARG* 4.7 4.6 - - - +
626B VAL* 3.3 51.9 + - - +
652B LEU* 4.4 10.5 - - + +
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Residues in contact with GLY 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B PHE 3.1 11.0 + - - -
608B LEU* 2.7 14.4 + - - -
610B LYS* 1.3 75.6 - - - +
612B TYR* 1.3 63.0 + - - +
614B GLU* 3.4 12.9 + - - +
615B ALA* 3.2 18.6 + - - +
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Residues in contact with TYR 612 (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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95A LEU* 4.9 4.9 - - - +
96A PHE* 3.2 40.6 + + + +
505B LEU* 3.4 38.4 + - + +
507B PHE* 3.8 30.5 - + + -
569B LEU* 3.9 19.3 - - + -
589B LEU* 6.4 0.2 - - + -
594B VAL* 4.6 5.5 - - + +
608B LEU* 3.0 39.4 + - + -
609B LEU* 3.5 9.9 - - + +
611B GLY* 1.3 74.4 - - - +
613B LEU* 1.3 65.5 + - + +
615B ALA* 2.8 18.9 + - + +
616B LEU* 2.9 13.1 + - - +
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Residues in contact with LEU 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B PHE* 5.4 7.2 - - + -
609B LEU* 2.9 53.3 + - + +
610B LYS 2.9 7.4 + - - +
612B TYR* 1.3 74.2 - - - +
614B GLU* 1.3 59.1 + - - +
616B LEU* 3.3 20.5 + - + +
617B PHE* 2.7 40.6 + - + -
624B PHE* 3.6 22.9 - - + -
652B LEU* 4.1 13.9 - - + -
671B PHE* 3.9 34.1 - - + -
673B LEU* 5.9 0.9 - - + -
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Residues in contact with GLU 614 (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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610B LYS* 2.8 55.4 + - + +
611B GLY* 3.7 9.4 - - - +
613B LEU* 1.3 72.4 - - - +
615B ALA* 1.3 57.7 + - - +
617B PHE* 3.2 4.3 + - - +
618B ALA* 2.9 27.6 + - - +
624B PHE* 3.1 30.2 - - + +
625B ARG* 5.8 0.2 - - - -
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Residues in contact with ALA 615 (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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505B LEU* 4.6 15.5 - - + -
611B GLY 3.2 12.2 + - - +
612B TYR* 2.8 12.8 + - + +
614B GLU* 1.3 72.1 - - - +
616B LEU* 1.3 61.7 + - - +
618B ALA* 3.1 10.8 + - - +
619B ARG* 2.9 28.2 + - - +
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Residues in contact with LEU 616 (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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498B LEU* 4.2 10.1 - - + -
501B VAL* 4.4 12.8 - - + -
502B LEU* 4.2 29.4 - - + -
505B LEU* 4.0 16.7 - - + +
507B PHE* 6.2 2.0 - - + -
585B LEU* 5.6 6.7 - - + -
612B TYR 2.9 9.9 + - - +
613B LEU* 3.3 20.4 - - + +
615B ALA* 1.3 77.1 - - - +
617B PHE* 1.3 82.2 + - + +
619B ARG* 2.9 11.2 + - - +
620B LEU* 2.8 54.9 + - + +
671B PHE* 6.2 1.6 - - + -
677B LEU* 5.9 1.3 - - + -
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Residues in contact with PHE 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B LEU* 2.7 37.8 + - + -
614B GLU 3.7 4.5 - - - +
616B LEU* 1.3 93.5 - - + +
618B ALA* 1.3 57.4 + - - +
620B LEU* 4.0 6.3 - - + +
621B GLY* 2.7 30.8 + - - -
622B LEU* 3.0 45.8 + - + +
624B PHE* 3.6 38.4 - + + +
642B VAL* 5.7 3.8 - - + -
644B VAL* 3.5 25.4 - - + -
673B LEU* 5.7 8.5 - - + -
677B LEU* 4.1 21.3 - - + -
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Residues in contact with ALA 618 (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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614B GLU 2.9 14.9 + - - +
615B ALA* 3.1 18.8 - - - +
617B PHE* 1.3 77.0 - - - +
619B ARG* 1.3 58.7 + - - +
621B GLY* 3.5 8.9 + - - -
622B LEU 5.1 0.7 - - - -
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Residues in contact with ARG 619 (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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501B VAL* 3.6 32.3 - - + +
505B LEU* 6.3 0.4 - - + -
615B ALA 2.9 11.4 + - - +
616B LEU* 2.9 14.6 + - - +
618B ALA* 1.3 77.5 - - - +
620B LEU* 1.3 61.4 + - + +
621B GLY 3.2 0.8 + - - -
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Residues in contact with LEU 620 (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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494B LYS* 4.7 18.2 - - - +
498B LEU* 4.7 7.2 - - + -
501B VAL* 4.4 22.0 - - + -
616B LEU* 2.8 45.5 + - + +
617B PHE* 3.0 8.7 + - + +
619B ARG* 1.3 81.9 - - + +
621B GLY* 1.3 62.6 + - - +
622B LEU* 3.5 22.7 + - + +
677B LEU* 3.9 28.0 - - + -
679B ASP* 5.0 7.4 - - - +
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Residues in contact with GLY 621 (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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617B PHE 2.7 7.9 + - - -
618B ALA* 3.5 8.1 + - - -
619B ARG 3.2 4.4 + - - -
620B LEU* 1.3 79.9 - - - +
622B LEU* 1.3 61.2 + - - +
679B ASP* 5.4 0.3 - - - +
680B LYS* 3.0 38.1 - - - +
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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