Contacts of the helix formed by residues 662 - 679 (chain B) in PDB entry 1L8A
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 TYR 662 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B THR* 4.1 4.7 - - - -
660B PRO* 4.3 0.2 - - - +
661B ALA* 1.3 90.0 - - + +
663B ALA* 1.3 66.9 + - - +
664B TYR* 3.4 45.3 - + + +
665B GLU* 2.9 29.8 + - - +
666B VAL* 3.2 14.4 + - - +
696B TYR* 4.3 8.1 - + - -
697B HIS 4.2 6.3 - - - -
698B MET* 3.7 9.4 - - - -
699B PRO* 3.6 26.5 - - + -
714B TYR* 4.6 0.2 - - - -
716B LEU* 4.1 5.2 - - + -
735B LEU* 3.6 24.8 - - + +
736B ARG* 4.8 9.8 - - + +
739B ARG* 2.9 45.4 + - - -
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Residues in contact with ALA 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU* 3.9 13.0 - - + +
488B GLN* 4.4 7.6 - - + -
492B ILE* 4.2 10.8 - - + -
497B ALA* 3.5 30.5 - - + +
662B TYR* 1.3 73.8 - - - +
664B TYR* 1.3 62.5 + - - +
666B VAL* 3.2 4.9 + - - +
667B ALA* 3.1 20.6 + - - +
698B MET* 3.4 33.1 - - + +
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Residues in contact with TYR 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU 3.2 20.5 + - - +
485B LEU* 3.7 12.0 - - + +
662B TYR* 3.4 28.7 - + + -
663B ALA* 1.3 78.6 - - - +
665B GLU* 1.3 74.1 + - + +
667B ALA* 3.4 2.5 + - - +
668B VAL* 3.1 27.5 + - - +
699B PRO* 3.0 32.4 - - + +
700B ALA 3.5 10.3 + - - -
701B MET* 3.3 40.4 - - + -
702B PRO* 3.5 16.5 - - + +
709B ILE* 3.7 8.7 - - + -
714B TYR* 2.6 30.4 + + - -
716B LEU* 3.7 8.7 - - - +
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Residues in contact with GLU 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B PRO* 3.7 10.6 - - + +
661B ALA* 2.8 33.1 + - - +
662B TYR* 2.9 21.1 + - + +
664B TYR* 1.3 93.6 - - + +
666B VAL* 1.3 66.8 + - - +
668B VAL* 3.2 1.4 + - - +
669B ILE* 2.9 31.1 + - + +
709B ILE* 4.0 17.0 - - + -
714B TYR* 2.5 27.4 + - - +
757B SER* 2.6 18.2 + - - -
759B THR* 3.6 15.9 - - + +
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Residues in contact with VAL 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B THR* 3.8 26.2 - - + +
497B ALA* 4.2 7.4 - - + +
498B PHE* 3.9 23.6 - - + +
660B PRO* 3.7 21.1 - - + -
662B TYR 3.6 12.1 - - - +
663B ALA 3.2 8.0 + - - +
665B GLU* 1.3 77.1 - - - +
667B ALA* 1.3 58.8 + - - +
669B ILE* 3.8 7.4 - - - +
670B MET* 2.9 54.0 + - + +
689B ILE* 5.3 4.9 - - + -
691B THR* 5.1 5.2 - - + -
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Residues in contact with ALA 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LEU* 4.4 2.4 - - - +
481B PHE* 4.2 13.2 - - + -
484B LEU* 3.7 40.4 - - + -
485B LEU* 4.0 10.8 - - + -
501B ALA* 5.0 3.6 - - - -
663B ALA 3.1 3.6 + - - +
664B TYR 3.5 9.0 - - - +
665B GLU 3.1 0.4 - - - -
666B VAL* 1.3 82.2 - - - +
668B VAL* 1.3 56.8 + - - +
670B MET* 3.5 3.7 + - - +
671B HIS* 3.0 30.7 + - - +
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Residues in contact with VAL 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LEU* 4.0 23.3 - - + -
485B LEU* 4.0 10.3 - - + -
664B TYR 3.1 17.5 + - - +
665B GLU 3.2 3.3 + - - +
667B ALA* 1.3 75.8 - - - +
669B ILE* 1.3 57.6 + - - +
671B HIS* 3.5 2.9 + - - +
672B ASP* 2.9 28.2 + - - +
701B MET* 4.0 9.0 - - - -
706B GLU* 3.7 26.7 - - + +
709B ILE* 3.8 27.4 - - + -
710B ARG* 4.0 21.3 - - + +
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Residues in contact with ILE 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B TYR* 3.6 60.8 - - + -
660B PRO* 3.9 25.6 - - + -
665B GLU 2.9 23.1 + - - +
666B VAL* 3.8 4.3 - - - +
668B VAL* 1.3 77.2 - - - +
670B MET* 1.3 57.5 + - - +
672B ASP* 3.3 5.5 + - - +
673B GLY* 2.8 27.4 + - - -
687B TYR* 3.7 9.6 - - + -
689B ILE* 3.8 21.5 - - + -
709B ILE* 3.9 17.5 - - + +
710B ARG* 5.5 2.0 - - - +
759B THR* 4.4 3.6 - - - -
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Residues in contact with MET 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B PHE* 5.5 0.4 - - + -
498B PHE* 3.6 33.7 - - + +
501B ALA* 3.4 31.6 - - + -
502B LEU* 4.3 4.3 - - - +
505B MET* 3.7 18.1 - - + +
595B PHE* 3.7 24.0 - - + -
622B PHE* 3.7 16.1 - - + -
624B ILE* 5.5 0.2 - - + -
666B VAL* 2.9 36.0 + - + +
667B ALA* 4.0 3.4 - - - +
669B ILE* 1.3 75.7 - - - +
671B HIS* 1.3 62.6 + - - +
673B GLY 3.5 0.3 + - - -
674B LEU* 3.0 24.6 + - - +
689B ILE* 3.9 20.2 - - + -
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Residues in contact with HIS 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B LEU* 6.1 0.4 - - + -
476B PRO* 3.2 27.9 + - + -
477B SER* 3.6 5.1 - - - -
478B LEU* 3.5 42.1 + - + +
481B PHE* 4.0 18.8 - + + -
505B MET* 4.9 0.2 - - - +
667B ALA 3.0 18.3 + - - +
668B VAL 3.8 4.1 + - - +
670B MET* 1.3 78.3 - - - +
672B ASP* 1.3 67.1 + - - +
674B LEU* 3.3 9.5 + - + +
675B GLU* 3.0 39.3 + - + +
710B ARG* 4.7 12.5 + - - -
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Residues in contact with ASP 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B TYR* 4.7 2.8 + - - +
668B VAL 2.9 19.6 + - - +
669B ILE* 3.6 5.4 - - - +
671B HIS* 1.3 80.3 + - - +
673B GLY* 1.3 59.9 + - - +
675B GLU* 3.2 7.5 + - - +
676B ARG* 2.9 60.5 + - - +
687B TYR* 3.6 5.9 + - - +
710B ARG* 3.5 44.5 + - + +
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Residues in contact with GLY 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B PHE* 4.1 5.4 - - - -
669B ILE 2.8 13.3 + - - -
670B MET 3.9 1.8 - - - -
672B ASP* 1.3 75.0 - - - +
674B LEU* 1.3 62.8 + - - +
676B ARG* 4.5 0.4 - - - -
677B MET* 3.0 36.7 + - - +
687B TYR* 3.4 34.7 + - - -
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Residues in contact with LEU 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B LEU* 3.8 14.0 - - + +
476B PRO* 3.6 37.9 - - + +
481B PHE* 4.8 2.0 - - + -
505B MET* 3.7 26.7 - - + -
511B ILE* 3.9 11.9 - - + -
593B ILE* 3.7 40.6 - - + -
622B PHE* 3.6 8.1 - - + -
670B MET 3.0 12.2 + - - +
671B HIS* 3.3 11.4 - - + +
673B GLY* 1.3 75.6 - - - +
675B GLU* 1.3 56.6 + - - +
677B MET* 4.8 1.3 - - - -
678B TYR* 2.9 36.9 + - + +
679B GLY 3.5 0.7 + - - -
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Residues in contact with GLU 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B LEU* 3.9 23.5 - - - +
476B PRO 4.9 0.9 - - - +
671B HIS* 3.0 28.7 + - + +
672B ASP* 3.6 13.0 - - - +
674B LEU* 1.3 80.8 - - - +
676B ARG* 1.3 59.3 + - + +
679B GLY* 2.9 45.7 + - - -
680B GLU* 4.3 5.0 + - - +
681B LYS* 4.3 4.8 - - + +
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Residues in contact with ARG 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B ILE* 4.1 29.1 - - - +
658B TYR* 4.4 5.3 + - - -
672B ASP* 2.9 39.3 + - - +
673B GLY* 3.8 3.4 - - - +
675B GLU* 1.3 74.1 - - + +
677B MET* 1.3 56.2 + - + +
681B LYS* 3.5 22.4 - - + +
682B GLN 3.3 9.7 + - - -
683B GLU* 2.7 78.9 + - + +
685B VAL* 4.5 1.7 - - + +
687B TYR* 2.8 44.3 + - + -
763B GLU* 5.1 4.9 + - - -
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Residues in contact with MET 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B PHE* 4.1 0.2 - - - -
620B ARG* 3.2 34.5 + - + -
621B GLY* 3.5 31.6 - - - +
622B PHE* 3.4 38.6 - - + -
673B GLY 3.0 23.6 + - - +
674B LEU* 4.8 0.2 - - - -
676B ARG* 1.3 78.0 - - + +
678B TYR* 1.3 74.0 + - + +
679B GLY 3.6 0.2 - - - -
682B GLN* 3.3 7.6 - - - -
683B GLU 3.8 7.6 - - - +
685B VAL* 3.1 40.4 - - + +
686B TYR* 3.9 3.6 - - - -
687B TYR* 4.0 9.4 - - + -
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Residues in contact with TYR 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B PHE* 3.5 26.7 - + - -
473B LEU* 3.5 24.9 + - + +
475B LEU* 3.6 8.3 - - + +
582B ALA 3.5 8.7 + - - -
585B TYR* 3.8 10.2 - + + -
591B PRO* 3.5 35.7 - - + -
592B MET 3.0 19.8 + - - -
593B ILE* 3.7 36.8 - - + -
620B ARG* 2.6 49.7 + - + +
674B LEU* 2.9 22.1 + - + +
677B MET* 1.3 84.2 - - + +
679B GLY* 1.3 62.3 + - - +
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Residues in contact with GLY 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B PHE* 4.6 1.2 - - - -
473B LEU 5.9 0.7 - - - -
475B LEU* 3.5 15.9 - - - -
674B LEU 3.5 1.2 + - - -
675B GLU* 2.9 25.4 + - - -
677B MET 3.6 0.2 - - - -
678B TYR* 1.3 82.3 - - - +
680B GLU* 1.3 68.4 + - - -
681B LYS 2.9 4.8 + - - -
682B GLN* 3.0 18.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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