Contacts of the helix formed by residues 652 - 666 (chain I) in PDB entry 5LS6
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 652 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263G ASN* 4.8 3.4 - - - +
265G ASP* 3.3 8.3 - - - +
609I GLY* 3.7 30.1 - - - +
612I GLU* 3.8 32.3 - - + -
613I VAL* 4.3 13.5 - - + +
616I LEU* 5.1 7.4 - - + -
647I ILE* 3.2 25.2 + - + +
650I LYS* 3.9 23.8 - - + +
651I ASN* 1.3 87.8 - - - +
653I CYS* 1.3 59.8 + - - +
654I ARG 3.3 2.9 - - - -
655I ASN* 4.0 10.3 - - + +
656I PHE* 3.1 28.4 + - - +
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Residues in contact with CYS 653 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G ASP* 3.1 6.9 + - - +
647I ILE* 4.3 3.6 - - - -
648I ILE* 4.1 33.9 - - - -
651I ASN* 5.0 8.1 - - - +
652I LEU* 1.3 80.8 - - - +
654I ARG* 1.3 59.5 + - + +
656I PHE* 3.9 6.7 - - - +
657I MET* 3.3 32.8 + - + +
681I LEU* 3.8 27.6 - - + +
682I ARG* 6.5 0.2 - - - -
685I GLN* 4.9 10.1 - - - +
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Residues in contact with ARG 654 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G ILE* 3.4 46.8 + - + -
265G ASP* 2.9 33.8 + - - +
266G GLY 4.9 0.2 - - - +
435G ALA* 4.0 15.5 - - - +
436G GLU* 6.2 1.8 - - - +
439G MET* 4.2 10.6 - - + +
460G THR* 5.3 10.5 - - - +
651I ASN* 4.9 6.7 + - - +
653I CYS* 1.3 79.0 - - + +
655I ASN* 1.3 55.2 + - - +
656I PHE 3.3 1.1 - - - -
657I MET* 3.1 19.6 - - + +
658I LEU* 2.8 36.3 + - - +
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Residues in contact with ASN 655 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263G ASN* 3.0 25.8 + - - +
264G ILE* 4.5 6.1 + - - +
265G ASP* 3.0 18.5 + - - +
281G PHE* 3.8 4.0 - - + -
607I ASN* 3.9 5.4 + - - -
609I GLY 2.9 23.4 + - - +
610I GLU* 3.8 12.9 - - - +
613I VAL* 3.7 21.1 - - + -
652I LEU* 4.0 10.7 - - + +
653I CYS 3.7 0.2 - - - -
654I ARG* 1.3 72.3 - - - +
656I PHE* 1.3 56.5 + - - +
658I LEU* 3.0 22.8 + - - +
659I HIS* 2.6 36.2 + - - +
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Residues in contact with PHE 656 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613I VAL* 3.9 14.4 - - + +
636I CYS* 4.8 3.6 - - + -
639I PHE* 3.6 34.3 - + - -
640I VAL* 3.3 32.1 - - + -
647I ILE* 4.4 10.3 - - + -
652I LEU 3.1 18.6 + - - +
653I CYS 3.9 3.6 - - - +
655I ASN* 1.3 78.5 - - - +
657I MET* 1.3 56.8 + - - +
659I HIS* 3.4 9.2 + + - +
660I LEU* 2.9 64.2 + - + +
677I ALA* 4.4 8.7 - - + -
678I VAL* 5.0 3.6 - - + -
681I LEU* 4.0 33.9 - - + -
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Residues in contact with MET 657 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439G MET* 3.5 31.9 - - + +
443G LEU* 5.6 1.6 - - + -
457G LEU* 3.3 30.3 - - + +
458G ILE* 5.1 3.4 - - - +
653I CYS* 3.3 26.7 + - + +
654I ARG* 3.1 21.7 + - + +
655I ASN 3.1 0.4 - - - -
656I PHE* 1.3 78.5 - - - +
658I LEU* 1.3 54.9 + - - +
660I LEU* 3.5 10.4 - - - +
661I VAL* 3.1 33.5 + - + +
674I ILE* 5.2 6.2 - - + +
678I VAL* 3.9 35.2 - - + -
681I LEU* 5.4 2.5 - - + -
682I ARG* 4.3 9.0 - - - +
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Residues in contact with LEU 658 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G ILE* 3.8 26.2 - - + -
277G SER* 4.1 11.0 - - - +
278G LEU* 3.4 26.7 - - + +
281G PHE* 3.7 22.9 - - + -
439G MET* 4.1 19.3 - - - -
442G VAL* 4.1 20.2 - - + -
610I GLU* 4.9 2.9 - - - +
654I ARG 2.8 18.8 + - - +
655I ASN* 3.0 28.7 + - - +
657I MET* 1.3 71.5 - - - +
659I HIS* 1.3 59.1 + - - +
661I VAL* 3.0 3.1 + - - -
662I SER* 2.8 27.5 + - - -
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Residues in contact with HIS 659 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G PHE* 3.6 19.4 - - + -
292G TYR* 2.6 29.3 + + - -
613I VAL* 4.3 9.9 - - + -
617I TRP* 3.2 54.8 - + + +
636I CYS* 4.8 0.6 - - - -
639I PHE* 4.9 2.9 - + - -
655I ASN 2.6 19.6 + - - +
656I PHE* 3.5 27.8 - + - +
658I LEU* 1.3 70.4 - - - +
660I LEU* 1.3 63.1 + - + +
662I SER* 3.3 3.1 + - - -
663I MET* 2.9 57.4 + - + +
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Residues in contact with LEU 660 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636I CYS* 3.8 34.8 - - + -
656I PHE* 2.9 51.9 + - + +
657I MET* 3.5 7.6 - - - +
659I HIS* 1.3 75.4 - - + +
661I VAL* 1.3 64.6 + - - +
663I MET* 3.1 7.4 + - - +
664I HIS* 2.9 19.9 + - - +
669I ILE* 3.4 15.3 - - + +
673I SER 5.1 1.6 - - - +
674I ILE* 4.2 23.6 - - + +
677I ALA* 4.3 7.9 - - + -
678I VAL* 3.8 28.0 - - + -
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Residues in contact with VAL 661 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G ARG* 3.6 17.0 - - - +
278G LEU* 3.6 27.8 - - + -
439G MET* 4.5 7.6 - - + -
442G VAL* 4.0 20.0 - - + -
443G LEU* 4.7 10.8 - - + -
446G THR* 4.4 15.5 - - + -
657I MET* 3.1 18.1 + - + +
658I LEU* 3.0 7.4 + - - +
660I LEU* 1.3 72.1 - - + +
662I SER* 1.3 55.9 + - - +
664I HIS* 3.0 8.7 + - - +
665I ASP* 2.7 35.0 + - - +
674I ILE* 5.0 10.3 - - + -
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Residues in contact with SER 662 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G LEU* 4.2 2.1 - - - +
281G PHE* 3.6 31.9 + - - +
282G HIS* 4.1 18.6 - - - -
285G PHE* 4.6 2.9 - - - -
292G TYR* 4.0 7.1 + - - -
658I LEU 2.8 10.0 + - - -
659I HIS* 3.3 10.3 + - - -
661I VAL* 1.3 74.4 - - - +
663I MET* 1.3 54.0 + - - +
665I ASP* 3.0 4.0 + - - +
666I PHE* 2.8 57.2 + - - -
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Residues in contact with MET 663 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G PHE* 3.6 29.4 - - - -
292G TYR* 5.1 0.4 - - - -
617I TRP* 3.8 11.7 - - + -
632I MET* 3.5 33.9 - - + -
636I CYS* 4.2 13.0 - - - -
659I HIS* 2.9 47.9 + - + +
660I LEU* 3.1 10.1 + - - +
662I SER* 1.3 75.9 + - - +
664I HIS* 1.3 60.2 + - - +
666I PHE* 3.2 9.6 + - - +
668I LEU* 3.1 42.3 + - + +
669I ILE* 3.8 15.7 - - + -
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Residues in contact with HIS 664 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G ARG* 3.2 68.0 + - + -
309G LYS 5.9 0.4 - - - -
446G THR* 2.8 31.6 + - - +
660I LEU 2.9 10.7 + - - +
661I VAL* 3.4 8.5 - - - +
663I MET* 1.3 72.9 - - - +
665I ASP* 1.3 70.4 + - - +
667I ASN 3.0 11.1 + - - -
669I ILE* 3.4 24.2 - - + +
671I ILE* 3.7 40.5 - - + +
674I ILE* 3.7 12.8 - - + -
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Residues in contact with ASP 665 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G ARG* 3.1 32.1 + - - -
282G HIS* 3.1 30.4 + - + -
305G THR 3.4 2.8 - - - +
306G TYR* 3.0 40.7 - - + +
307G LYS* 3.7 2.6 + - - +
308G ARG* 4.0 10.5 + - - +
446G THR* 4.0 11.3 + - - -
661I VAL* 2.7 16.9 + - - +
662I SER 3.2 8.1 - - - +
664I HIS* 1.3 73.2 + - - +
666I PHE* 1.3 57.7 + - - +
667I ASN* 3.1 11.1 + - - +
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Residues in contact with PHE 666 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G HIS* 3.4 34.8 - - - -
285G PHE* 3.5 43.1 - + + -
287G ARG* 4.0 23.1 + - + -
301G ALA* 4.5 3.8 - - + -
305G THR* 3.6 40.0 + - + +
306G TYR* 3.9 16.6 - + + -
662I SER* 2.8 47.1 + - - -
663I MET 3.5 8.7 - - - +
664I HIS 3.2 0.8 - - - -
665I ASP* 1.3 69.8 - - - +
667I ASN* 1.3 68.7 + - - +
668I LEU* 3.1 22.2 - - + +
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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