Contacts of the helix formed by residues 652 - 666 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D ASN* 5.1 1.6 - - - +
265D ASP* 3.6 8.3 - - - -
609F GLY* 3.8 28.5 - - - +
612F GLU* 4.2 24.0 - - + -
613F VAL* 4.3 14.0 - - + +
616F LEU* 4.5 9.9 - - + -
647F ILE* 3.2 24.5 + - + +
650F LYS* 3.7 31.0 - - + +
651F ASN* 1.3 89.1 - - - +
653F CYS* 1.3 60.6 + - - +
654F ARG 3.4 2.2 - - - -
655F ASN* 4.2 13.9 - - + +
656F PHE* 3.0 28.2 + - - +
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Residues in contact with CYS 653 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D ASP* 3.2 5.5 + - - +
647F ILE* 4.2 6.3 - - - -
648F ILE* 4.5 24.9 - - - -
651F ASN* 5.5 4.3 - - - -
652F LEU* 1.3 79.7 - - - +
654F ARG* 1.3 65.4 + - + +
656F PHE* 3.3 6.6 + - - +
657F MET* 3.0 35.2 + - + +
681F LEU* 4.3 21.4 - - + +
682F ARG* 6.0 3.8 - - - +
685F GLN* 4.5 17.7 - - - +
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Residues in contact with ARG 654 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D ILE* 3.4 38.8 + - + +
265D ASP* 2.8 34.6 + - - +
435D ALA* 4.4 13.0 - - - +
436D GLU* 6.1 1.4 - - - +
439D MET* 4.2 11.8 - - + +
458D ILE 5.8 1.2 + - - -
460D THR* 5.2 14.6 - - - +
651F ASN* 4.5 10.1 + - - +
653F CYS* 1.3 79.7 - - + +
655F ASN* 1.3 64.8 + - - +
657F MET* 3.5 14.1 + - + +
658F LEU* 3.2 24.1 + - - +
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Residues in contact with ASN 655 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ASN* 3.0 28.0 - - - +
264D ILE* 4.1 9.2 - - - +
265D ASP* 2.7 17.8 + - - +
281D PHE* 4.1 4.2 - - + -
607F ASN* 3.9 4.0 + - - +
609F GLY* 3.5 20.6 + - - -
610F GLU* 3.7 14.9 - - - +
613F VAL* 4.0 20.6 - - + +
652F LEU* 4.2 10.6 - - - +
653F CYS 3.4 0.2 - - - -
654F ARG* 1.3 71.2 - - - +
656F PHE* 1.3 64.7 + - - +
657F MET 3.1 1.6 - - - -
658F LEU* 3.0 24.2 + - - +
659F HIS* 3.0 22.9 + - - +
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Residues in contact with PHE 656 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613F VAL* 4.3 10.6 - - + +
636F CYS* 4.5 4.0 - - + -
639F PHE* 3.4 38.6 - + + -
640F VAL* 3.3 32.5 - - + -
647F ILE* 4.2 13.7 - - + -
652F LEU 3.0 21.2 + - - +
653F CYS 3.5 5.2 - - - +
655F ASN* 1.3 76.1 - - - +
657F MET* 1.3 61.2 + - - +
659F HIS* 3.6 10.9 - + - +
660F LEU* 3.4 54.5 + - + +
677F ALA* 4.3 11.7 - - + -
678F VAL* 4.8 4.0 - - + -
681F LEU* 3.9 23.8 - - + -
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Residues in contact with MET 657 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D MET* 3.4 33.9 - - + +
457D LEU* 3.5 26.7 - - - +
458D ILE 5.8 0.2 - - - +
653F CYS* 3.0 24.7 + - + +
654F ARG* 3.6 15.0 - - + +
655F ASN 3.1 0.4 - - - -
656F PHE* 1.3 75.4 - - - +
658F LEU* 1.3 58.1 + - - +
660F LEU* 3.2 9.6 + - - +
661F VAL* 3.0 32.1 + - + +
674F ILE* 4.8 9.4 - - + -
678F VAL* 3.4 44.0 - - + -
681F LEU* 5.9 1.6 - - + -
682F ARG* 3.6 15.9 - - - +
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Residues in contact with LEU 658 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D ILE* 3.6 31.2 - - + -
277D SER* 3.4 24.0 - - - +
278D LEU* 3.3 23.6 - - + +
281D PHE* 3.5 21.8 - - + -
439D MET* 4.4 9.4 - - - -
442D VAL* 4.1 22.0 - - + -
610F GLU* 4.0 5.2 - - - +
654F ARG 3.2 17.0 + - - +
655F ASN* 3.0 21.9 + - - +
657F MET* 1.3 71.2 - - - +
659F HIS* 1.3 56.2 + - - +
661F VAL* 3.2 3.3 + - - -
662F SER* 2.8 32.8 + - - -
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Residues in contact with HIS 659 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D PHE* 4.0 18.9 - - + -
292D TYR* 2.8 29.0 + + - -
613F VAL* 4.5 10.6 - - + +
617F TRP* 3.3 60.4 - + + +
636F CYS* 4.6 0.6 - - - -
639F PHE* 5.4 1.3 - + - -
655F ASN 3.0 11.2 + - - +
656F PHE* 3.6 22.7 - + - +
658F LEU* 1.3 76.0 - - - +
660F LEU* 1.3 66.2 + - + +
662F SER* 3.3 2.5 + - - -
663F MET* 2.7 59.4 + - + +
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Residues in contact with LEU 660 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636F CYS* 3.7 35.9 - - + -
656F PHE* 3.4 49.8 + - + +
657F MET* 3.2 9.2 + - - +
659F HIS* 1.3 80.4 - - + +
661F VAL* 1.3 58.1 + - - +
663F MET* 4.1 3.1 - - - -
664F HIS* 2.8 29.3 + - - +
669F ILE* 3.4 13.4 - - + +
673F SER 5.0 2.2 - - - +
674F ILE* 3.9 21.7 - - + +
677F ALA* 4.0 12.8 - - + -
678F VAL* 3.9 22.2 - - + -
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Residues in contact with VAL 661 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ARG* 3.1 31.4 - - - +
278D LEU* 3.7 7.2 - - + -
439D MET* 4.8 2.5 - - + -
442D VAL* 3.7 27.8 - - + -
443D LEU* 4.3 18.6 - - + -
446D THR* 4.5 12.6 - - + -
657F MET 3.0 14.8 + - - +
658F LEU 3.2 7.2 + - - +
660F LEU* 1.3 74.3 - - - +
662F SER* 1.3 68.3 + - - +
664F HIS* 3.1 6.4 + - - +
665F ASP* 2.8 27.8 + - - +
674F ILE* 4.8 11.0 - - + -
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Residues in contact with SER 662 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D LEU* 4.1 2.1 - - - +
281D PHE* 3.7 25.3 - - - +
282D HIS* 4.0 20.2 - - - -
285D PHE* 4.6 2.8 - - - -
292D TYR* 3.7 11.4 + - - -
658F LEU 2.8 17.0 + - - -
659F HIS* 3.4 10.4 + - - -
661F VAL* 1.3 69.2 - - - +
663F MET* 1.3 59.7 + - - +
665F ASP* 2.8 24.3 + - - +
666F PHE* 2.9 30.9 + - - -
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Residues in contact with MET 663 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D PHE* 3.3 36.6 - - - -
617F TRP* 3.7 12.3 - - + -
632F MET* 3.5 38.6 - - + -
636F CYS* 4.0 14.4 - - - -
659F HIS* 2.7 47.5 + - + +
660F LEU* 3.5 6.1 - - - +
662F SER* 1.3 76.5 + - - +
664F HIS* 1.3 60.1 + - - +
666F PHE* 3.5 8.5 + - - +
668F LEU* 3.3 33.9 + - + +
669F ILE* 3.7 15.6 + - + -
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Residues in contact with HIS 664 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D ARG* 2.7 74.2 + - + +
446D THR* 2.7 30.3 + - - +
660F LEU 2.8 20.3 + - - +
661F VAL* 3.5 6.3 - - - +
663F MET* 1.3 69.3 - - - +
665F ASP* 1.3 70.5 + - - +
667F ASN* 2.9 4.5 + - - -
669F ILE* 3.2 18.3 - - + +
670F SER 3.7 0.7 - - - -
671F ILE* 3.3 42.4 + - + +
674F ILE* 3.7 13.0 - - + -
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Residues in contact with ASP 665 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ARG* 3.1 38.0 + - - -
278D LEU* 3.8 2.1 - - - +
282D HIS* 3.1 25.6 + - + -
305D THR 3.1 10.4 - - - +
306D TYR* 3.1 29.4 - - - +
307D LYS* 3.5 9.5 - - - +
308D ARG* 4.2 9.4 + - - +
446D THR* 4.2 2.9 + - - -
661F VAL 2.8 14.9 + - - +
662F SER 2.8 16.4 + - - +
664F HIS* 1.3 81.1 + - - +
666F PHE* 1.3 55.7 + - - +
667F ASN* 3.0 8.3 + - - +
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Residues in contact with PHE 666 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D HIS* 3.5 40.6 - - - -
285D PHE* 3.5 50.5 - + + -
287D ARG* 4.0 17.6 + - + -
301D ALA* 4.3 3.1 - - + -
305D THR* 3.3 55.0 + - + +
306D TYR* 3.9 10.5 - + + +
662F SER* 2.9 37.4 + - - -
663F MET 3.8 8.7 - - - +
664F HIS 3.2 0.6 - - - -
665F ASP* 1.3 74.0 - - - +
667F ASN* 1.3 66.1 + - - +
668F LEU* 3.5 19.1 - - + +
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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
------------------------------------------------------------
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