Contacts of the helix formed by residues 665 - 688 (chain A) in PDB entry 4L6V
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 LEU 665 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A ASN 5.4 2.9 - - - +
660A SER* 3.2 22.3 + - - -
663A SER* 3.0 12.4 - - - +
664A ALA* 1.3 83.6 - - + +
666A SER* 1.3 62.8 + - - +
667A ALA 3.0 3.6 - - - -
668A TYR* 3.0 34.0 + - + +
669A GLY 3.4 1.0 + - - -
745A ALA* 4.4 11.4 - - + +
748A LEU* 3.8 35.2 - - + -
749A SER* 3.4 26.5 - - - +
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Residues in contact with SER 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.0 1.6 - - - +
126A LEU* 3.4 14.4 - - - +
660A SER* 3.1 21.4 + - - -
661A TYR* 4.2 2.7 - - - +
662A GLY 3.9 1.1 - - - -
663A SER 3.1 16.9 + - - -
664A ALA 3.2 0.8 - - - -
665A LEU* 1.3 78.8 - - - +
667A ALA* 1.3 66.1 + - - +
669A GLY* 3.1 9.2 + - - -
670A ILE* 3.3 18.5 + - - +
443B ALA* 3.1 33.0 + - - +
444B PHE* 3.9 9.8 - - - -
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Residues in contact with ALA 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.6 29.8 - - + +
664A ALA 4.8 2.0 - - - +
665A LEU 3.0 1.7 - - - -
666A SER* 1.3 81.9 + - - +
668A TYR* 1.3 66.2 + - + +
669A GLY 3.1 0.7 + - - -
670A ILE* 3.1 15.5 - - + +
671A MET* 2.8 33.6 + - - +
444B PHE* 5.8 0.9 - - - -
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Residues in contact with TYR 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 4.8 11.1 - - + +
138A GLN 4.4 8.7 + - - -
657A VAL* 3.1 12.6 - - - +
664A ALA 5.4 1.6 - - - -
665A LEU* 3.0 41.8 + - + +
667A ALA* 1.3 82.1 - - + +
669A GLY* 1.3 56.9 + - - +
671A MET* 4.0 5.4 - - - -
672A PHE* 2.8 23.0 + - - +
740A TRP* 3.8 27.7 - + - -
741A ALA* 3.4 25.2 - - + +
744A LEU* 3.3 44.5 - - + +
745A ALA* 4.0 13.9 - - + -
748A LEU* 4.0 10.9 - - + +
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Residues in contact with GLY 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A VAL* 3.3 12.7 - - - -
658A ILE* 5.4 1.1 - - - -
660A SER* 3.0 26.4 + - - -
661A TYR* 4.0 13.8 - - - -
666A SER 3.1 5.2 + - - -
667A ALA 3.1 1.6 - - - -
668A TYR* 1.3 79.1 - - - +
670A ILE* 1.3 59.8 + - - +
672A PHE* 3.4 15.2 + - - +
673A LEU* 3.6 11.4 + - - +
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Residues in contact with ILE 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A TYR* 3.2 32.5 - - + +
666A SER 3.3 7.1 + - - +
667A ALA* 3.1 20.0 - - - +
669A GLY* 1.3 75.0 - - - +
671A MET* 1.3 65.1 + - + +
672A PHE 3.3 0.4 - - - -
673A LEU* 3.4 8.7 + - + +
674A ALA* 2.9 25.6 + - - +
439B ASP* 4.0 11.2 - - + +
440B VAL* 4.3 20.9 - - + +
443B ALA* 3.6 19.7 - - + -
444B PHE* 5.1 14.1 - - + -
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Residues in contact with MET 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A ALA* 2.8 21.2 + - - +
668A TYR* 3.9 9.0 - - - +
670A ILE* 1.3 82.5 - - + +
672A PHE* 1.3 64.6 + - - +
673A LEU 3.2 0.4 - - - -
674A ALA* 3.6 27.5 - - + +
675A GLY* 3.1 18.9 + - - -
737A VAL* 3.3 23.5 - - + +
740A TRP* 3.7 26.0 - - + -
741A ALA* 4.1 6.5 - - + -
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Residues in contact with PHE 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A ALA* 5.0 9.2 - - + -
657A VAL* 3.5 26.9 - - + -
658A ILE* 4.2 21.5 - - + -
668A TYR 2.8 19.0 + - - +
669A GLY 3.4 8.5 - - - +
671A MET* 1.3 78.3 - - - +
673A LEU* 1.3 69.6 + - + +
675A GLY* 3.9 0.5 + - - -
676A HIS* 2.9 47.9 + + - -
738A THR* 3.5 41.4 + - + +
741A ALA* 3.7 7.1 - - + +
742A PHE* 4.2 14.8 - + + -
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Residues in contact with LEU 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A TYR* 3.8 23.3 - - + +
669A GLY 3.6 10.0 + - - +
670A ILE* 3.4 10.6 + - + +
671A MET 3.2 0.2 - - - -
672A PHE* 1.3 89.2 - - + +
674A ALA* 1.3 64.6 + - - +
675A GLY 3.2 0.2 - - - -
676A HIS* 2.9 25.0 + - + +
677A PHE* 3.0 13.4 + - - +
439B ASP* 4.1 17.0 - - + +
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Residues in contact with ALA 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A ILE 2.9 15.8 + - - +
671A MET* 3.3 30.2 + - + +
673A LEU* 1.3 74.5 - - - +
675A GLY* 1.3 62.9 + - - +
677A PHE* 3.1 16.5 + - - +
678A VAL* 3.3 20.7 + - + +
737A VAL* 4.7 2.9 - - + -
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Residues in contact with GLY 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A MET 3.1 12.4 + - - -
672A PHE 3.9 0.6 + - - -
674A ALA* 1.3 77.1 - - - +
676A HIS* 1.3 60.5 + - - +
678A VAL* 3.4 1.3 - - - +
679A PHE* 3.1 20.3 + - - +
734A GLY* 3.2 18.4 - - - -
737A VAL* 3.7 27.5 - - - +
738A THR* 3.6 10.8 - - - -
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Residues in contact with HIS 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A PHE* 2.9 44.0 + + - +
673A LEU* 2.9 19.5 + - + +
675A GLY* 1.3 75.2 - - - +
677A PHE* 1.3 62.5 + - - +
679A PHE* 3.4 13.4 - + - +
680A ALA* 3.2 21.3 + - - +
738A THR* 3.4 28.5 - - + +
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Residues in contact with PHE 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A LEU 3.0 11.2 + - - +
674A ALA* 3.1 12.3 + - - +
676A HIS* 1.3 77.0 - - - +
678A VAL* 1.3 70.9 + - + +
680A ALA* 3.1 8.5 + - - +
681A PHE* 2.9 43.2 + + + +
432B LEU* 3.6 43.1 - - + -
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Residues in contact with VAL 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A ALA* 3.3 12.1 + - + +
675A GLY* 3.4 4.7 - - - +
677A PHE* 1.3 81.8 - - + +
679A PHE* 1.3 64.2 + - - +
681A PHE* 3.5 13.2 - - + +
682A SER* 2.9 28.2 + - - -
730A HIS* 3.6 16.9 - - + +
733A LEU* 4.1 19.7 - - + -
734A GLY* 3.2 33.2 - - - +
737A VAL* 5.4 0.9 - - + -
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Residues in contact with PHE 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A GLY 3.1 19.3 + - - +
676A HIS* 3.4 14.8 - + - +
678A VAL* 1.3 78.6 - - - +
680A ALA* 1.3 77.7 + - + +
682A SER* 2.6 26.9 + - - -
683A LEU* 3.5 24.2 + - + +
730A HIS 4.5 6.1 - - - -
731A TYR* 3.3 50.7 - + - +
734A GLY* 4.6 7.0 - - - -
735A GLY* 5.0 7.0 - - - -
738A THR* 5.6 0.7 - - - +
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Residues in contact with ALA 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A HIS 3.2 7.7 + - - +
677A PHE* 3.1 9.7 + - - +
679A PHE* 1.3 90.1 - - + +
681A PHE* 1.3 61.0 + - - +
683A LEU* 3.0 29.9 + - + +
684A MET* 3.7 3.6 + - - +
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Residues in contact with PHE 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A PHE* 2.9 34.6 + + + +
678A VAL* 3.5 14.4 - - + +
679A PHE 3.2 0.2 - - - -
680A ALA* 1.3 77.2 - - - +
682A SER* 1.3 61.3 + - - +
684A MET* 3.2 45.0 + - + +
685A PHE* 3.4 26.9 - + - -
730A HIS* 3.2 38.4 - + - -
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Residues in contact with SER 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678A VAL 2.9 6.0 + - - -
679A PHE 2.6 19.5 + - - -
681A PHE* 1.3 78.9 - - - +
683A LEU* 1.3 60.7 + - - +
685A PHE* 3.1 18.6 + - - +
686A LEU* 3.1 17.0 + - - +
727A GLY* 3.4 12.5 - - - -
730A HIS* 3.5 12.1 - - - +
731A TYR* 3.2 49.3 - - - -
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Residues in contact with LEU 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A PHE* 3.6 22.0 - - + +
680A ALA* 3.0 25.4 + - + +
682A SER* 1.3 88.3 + - - +
684A MET* 1.3 64.8 + - - +
686A LEU* 3.8 7.2 - - + +
687A PHE* 3.2 63.4 + - + +
731A TYR* 3.9 22.9 - - + -
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Residues in contact with MET 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A ALA 3.7 3.2 + - - +
681A PHE* 3.2 41.4 + - - +
682A SER 3.1 0.2 - - - -
683A LEU* 1.3 80.0 - - - +
685A PHE* 1.3 68.9 + - + +
687A PHE* 4.9 0.4 - - - +
688A SER* 2.9 26.7 + - - -
693A TRP* 3.2 41.7 + - + +
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Residues in contact with PHE 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A PHE* 3.4 52.9 - + - -
682A SER* 3.1 9.3 + - - +
684A MET* 1.3 90.0 - - + +
686A LEU* 1.3 63.2 + - - +
687A PHE 3.3 1.1 + - - -
688A SER* 3.6 17.6 + - - +
693A TRP* 5.9 0.2 - - - +
718A LEU* 4.1 22.0 - - + -
723A GLY* 3.5 28.7 - - - +
724A ARG* 5.6 1.2 - - - +
726A VAL* 3.8 32.1 - - + -
727A GLY* 3.9 6.7 - - - -
730A HIS* 4.9 0.7 - + - -
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Residues in contact with LEU 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A PHE* 3.6 31.9 - - + -
596A PHE* 3.8 23.8 - - + -
682A SER* 3.1 27.4 + - - +
683A LEU* 3.5 6.0 + - + +
685A PHE* 1.3 76.9 - - - +
687A PHE* 1.3 75.0 + - + +
688A SER 4.6 1.9 - - - +
724A ARG* 4.3 4.3 - - - +
727A GLY* 3.6 35.4 - - - +
728A VAL 3.8 0.9 - - - +
731A TYR* 4.0 7.9 - - + -
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Residues in contact with PHE 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A LEU* 3.2 54.3 + - + +
684A MET 4.9 0.4 - - - +
686A LEU* 1.3 91.1 - - + +
688A SER* 1.3 59.9 + - - +
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Residues in contact with SER 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A MET 2.9 19.8 + - - -
685A PHE* 3.6 15.4 + - - +
686A LEU 3.6 1.8 - - - +
687A PHE* 1.3 81.4 + - - +
689A GLY* 1.3 58.7 + - - +
692A TYR* 5.9 3.6 - - - -
693A TRP* 2.8 32.2 + - - -
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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
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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