Contacts of the helix formed by residues 645 - 660 (chain N) in PDB entry 5L4K
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 ASN 645 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607N VAL* 3.5 29.5 - - + +
615N ARG* 3.7 27.2 + - - +
644N TYR* 1.3 97.7 - - + +
646N PRO* 1.3 66.0 - - - +
647N HIS* 3.1 23.6 + - - +
648N VAL* 2.5 51.4 + - + +
649N ARG* 3.5 5.9 + - - +
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Residues in contact with PRO 646 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645N ASN* 1.3 84.1 - - - +
647N HIS* 1.3 60.2 + - - +
649N ARG* 3.0 32.0 + - - +
650N TYR* 3.0 20.8 + - - +
680N VAL* 4.0 22.2 - - + -
682N TYR* 3.1 33.9 - - + +
683N VAL* 3.6 6.4 - - + +
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Residues in contact with HIS 647 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610N VAL* 4.0 8.1 - - + -
612N ASP* 3.3 33.6 + - + +
615N ARG* 3.1 52.4 + - + -
616N ARG* 4.3 14.5 + - + +
645N ASN* 2.6 13.4 + - - +
646N PRO* 1.3 77.0 - - + +
648N VAL* 1.3 61.6 + - - +
650N TYR* 3.3 6.9 + - + +
651N GLY* 3.0 19.8 + - - -
682N TYR* 3.4 33.6 + + - -
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Residues in contact with VAL 648 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603N LEU* 4.2 19.5 - - + -
606N ALA* 6.0 0.4 - - + -
607N VAL* 4.8 2.9 - - + -
615N ARG* 4.6 18.4 - - + +
619N VAL* 4.1 6.8 - - + +
640N LEU* 3.0 46.7 - - + +
643N SER* 5.1 5.8 - - - +
644N TYR 4.5 4.7 - - - +
645N ASN* 2.5 41.0 + - + +
647N HIS* 1.3 68.3 - - - +
649N ARG* 1.3 65.0 + - - +
651N GLY* 3.1 2.8 + - - +
652N ALA* 2.9 21.1 + - - +
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Residues in contact with ARG 649 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640N LEU 4.5 4.9 - - - -
641N SER* 3.2 30.2 + - - +
642N GLU 4.4 3.4 + - - -
643N SER 3.6 17.2 + - - +
644N TYR* 3.8 8.7 - - - +
645N ASN 3.5 9.4 + - - +
646N PRO* 3.0 50.3 + - - +
648N VAL* 1.3 77.5 - - - +
650N TYR* 1.3 66.2 + - - +
652N ALA* 2.8 15.9 + - - +
653N ALA* 2.9 12.8 + - - +
675N MET* 3.8 13.9 - - + +
678N ASP* 2.9 38.4 + - - -
680N VAL* 5.0 0.6 - - - +
683N VAL* 3.7 18.5 - - + +
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Residues in contact with TYR 650 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616N ARG* 3.5 46.6 + - + +
620N GLU* 6.4 0.4 - - + -
646N PRO 3.0 10.0 + - - +
647N HIS* 3.5 10.1 - - - +
649N ARG* 1.3 76.7 - - - +
651N GLY* 1.3 69.0 + - - +
653N ALA* 2.9 18.2 + - - +
654N MET* 3.0 34.7 + - + +
682N TYR* 3.9 25.1 - + + +
683N VAL* 4.4 8.4 - - + +
685N GLN* 4.9 7.0 - - + -
686N GLY* 3.8 30.7 - - - -
689N ILE* 6.2 0.2 - - + -
767N THR* 3.8 18.2 + - - +
769N PHE* 4.8 7.4 + - - -
770N TRP* 3.9 12.0 - + - -
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Residues in contact with GLY 651 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616N ARG* 3.7 22.7 - - - -
619N VAL* 3.2 11.1 - - - +
620N GLU* 3.5 8.5 + - - -
647N HIS 3.0 14.0 + - - -
648N VAL 3.6 2.7 - - - -
650N TYR* 1.3 84.3 - - - +
652N ALA* 1.3 57.1 + - - +
654N MET* 3.3 2.9 + - - -
655N ALA* 2.8 26.5 + - - +
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Residues in contact with ALA 652 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619N VAL* 3.0 17.3 - - + +
637N VAL* 4.3 14.5 - - + +
640N LEU* 4.3 10.1 - - + +
641N SER* 3.5 23.3 - - - +
648N VAL 2.9 10.9 + - - +
649N ARG 2.8 12.5 + - - +
651N GLY* 1.3 72.3 - - - +
653N ALA* 1.3 58.3 + - - +
655N ALA* 3.0 6.5 + - - +
656N LEU* 2.9 32.8 + - - +
675N MET* 4.7 0.7 - - - -
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Residues in contact with ALA 653 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649N ARG 2.9 7.2 + - - +
650N TYR* 3.4 10.8 - - - +
652N ALA* 1.3 78.1 - - - +
654N MET* 1.3 55.6 + - - +
656N LEU* 3.9 4.9 - - - +
657N GLY 2.9 20.8 + - - -
672N LEU* 4.8 4.3 - - + -
675N MET* 3.7 23.1 - - + +
683N VAL* 5.5 1.1 - - + +
686N GLY 3.2 27.6 - - - +
687N ALA* 4.3 5.2 - - + +
690N ALA* 3.1 19.4 - - + +
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Residues in contact with MET 654 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620N GLU* 4.1 11.6 - - + +
650N TYR* 3.0 37.3 + - + +
651N GLY 3.6 5.8 - - - +
653N ALA* 1.3 74.5 - - - +
655N ALA* 1.3 63.5 + - - +
656N LEU 3.3 0.9 - - - -
657N GLY* 3.9 2.9 - - - +
658N ILE* 3.3 33.2 + - + +
686N GLY* 4.0 17.9 - - - +
689N ILE* 4.1 17.9 - - + -
690N ALA* 4.5 2.9 - - - -
693N LEU* 4.2 21.5 - - + -
766N PHE* 5.1 2.5 - - + -
767N THR* 2.9 51.4 - - + +
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Residues in contact with ALA 655 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619N VAL* 3.2 26.0 - - + +
620N GLU* 4.4 1.8 - - - +
622N LEU* 4.2 8.3 - - + -
623N GLY* 3.3 28.9 - - - +
633N CYS* 3.7 12.0 - - - -
637N VAL* 4.2 10.3 - - + -
651N GLY 2.8 9.6 + - - +
652N ALA* 3.0 16.1 + - - +
654N MET* 1.3 78.3 - - - +
656N LEU* 1.3 58.6 + - - +
659N CYS* 3.7 7.6 + - - -
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Residues in contact with LEU 656 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633N CYS* 3.5 31.9 - - + -
634N PRO* 4.6 3.1 - - + -
637N VAL* 3.8 23.6 - - + -
641N SER* 5.4 0.7 - - - +
652N ALA 2.9 16.4 + - - +
653N ALA 3.9 1.1 - - - +
655N ALA* 1.3 75.5 - - - +
657N GLY* 1.3 66.4 + - - +
658N ILE 3.0 3.8 + - - -
660N CYS* 3.2 30.5 + - - +
668N ALA* 4.3 25.4 - - + +
671N LEU* 4.5 13.5 - - + -
672N LEU* 3.3 34.1 - - + -
675N MET* 4.9 7.0 - - - -
694N ILE* 4.1 6.8 - - + +
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Residues in contact with GLY 657 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653N ALA 2.9 18.9 + - - -
654N MET* 3.9 4.7 + - - -
655N ALA 3.7 0.4 - - - -
656N LEU* 1.3 75.4 - - - +
658N ILE* 1.3 60.6 + - - +
661N ALA* 3.2 22.2 - - - +
690N ALA* 3.7 27.3 - - - +
693N LEU* 3.6 17.7 - - - +
694N ILE* 4.2 2.0 + - - +
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Residues in contact with ILE 658 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620N GLU* 4.5 12.3 - - + -
623N GLY* 4.1 15.9 - - - +
624N PHE* 4.1 27.6 - - + -
627N PHE* 5.7 0.6 - - + -
654N MET* 3.3 24.3 + - + +
656N LEU 3.0 1.2 + - - -
657N GLY* 1.3 80.6 - - - +
659N CYS* 1.3 65.8 + - - +
661N ALA* 3.5 12.0 + - - +
662N GLY 4.3 2.3 + - - -
693N LEU* 5.0 4.5 - - + -
746N ILE* 5.1 3.0 - - - +
748N LEU* 3.9 26.3 - - + +
763N VAL* 3.8 35.9 - - + +
764N LEU* 6.0 0.2 - - + -
767N THR* 4.1 20.2 - - - +
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Residues in contact with CYS 659 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623N GLY* 3.3 23.3 - - - +
626N LEU 3.5 25.6 - - - +
627N PHE* 4.0 20.0 - - + -
630N PRO* 3.2 19.9 - - + +
633N CYS* 3.7 34.5 - - - -
655N ALA 3.7 7.9 + - - +
656N LEU 3.4 2.0 + - - -
658N ILE* 1.3 76.3 - - - +
660N CYS* 1.3 66.7 + - - +
661N ALA 3.2 7.4 + - - -
662N GLY* 3.8 7.8 + - - -
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Residues in contact with CYS 660 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630N PRO 3.4 27.1 - - - -
631N GLU* 4.8 1.3 - - - -
633N CYS* 3.8 28.3 - - - -
634N PRO* 4.2 9.9 - - - -
656N LEU* 3.2 20.0 + - + +
659N CYS* 1.3 80.1 - - - +
661N ALA* 1.3 57.9 + - - +
662N GLY 3.6 0.4 - - - -
663N THR* 4.1 8.7 - - + -
664N GLY* 3.4 17.2 + - - -
665N ASN* 3.9 3.8 + - - +
668N ALA* 4.1 19.7 - - + -
694N ILE* 3.6 16.4 - - + +
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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