Contacts of the helix formed by residues 646 - 664 (chain J) in PDB entry 4XLN
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 LYS 646 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H GLN* 6.1 1.2 - - - +
644J LEU 3.4 0.8 + - - -
645J PRO* 1.3 68.9 - - - +
647J ARG* 1.3 98.5 + - + +
649J ALA* 3.1 2.8 + - - +
650J LEU* 2.9 25.3 + - - +
683J ILE* 4.7 2.6 - - - +
688J TRP* 3.5 49.6 - - + +
720J LEU* 3.7 18.0 - - + +
721J VAL 3.1 18.0 + - - +
722J GLU* 3.3 39.6 + - + +
723J GLY 4.6 6.5 - - - +
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Residues in contact with ARG 647 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005I MET* 5.0 13.9 - - + -
645J PRO* 5.2 1.3 - - + -
646J LYS* 1.3 110.3 - - + +
648J MET* 1.3 66.5 + - - +
650J LEU* 3.3 11.4 + - - +
651J GLU* 3.4 13.3 + - - +
681J ARG* 3.8 39.9 - - - +
683J ILE* 3.3 33.3 - - - +
688J TRP* 4.7 4.4 - - - -
724J GLN* 5.3 16.3 - - + +
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Residues in contact with MET 648 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005I MET* 3.6 31.4 - - + +
1006I HIS 3.3 22.0 - - - +
1007I ALA* 3.6 20.9 - - + +
627J GLY* 5.1 0.9 - - - -
628J ARG 3.4 19.7 - - - +
629J SER* 3.7 9.9 - - - +
644J LEU* 3.7 25.4 - - + -
645J PRO* 3.5 18.0 + - + +
646J LYS 3.4 0.2 - - - -
647J ARG* 1.3 79.4 - - - +
649J ALA* 1.3 59.0 + - - +
651J GLU* 3.6 3.4 + - - +
652J LEU* 2.9 34.3 + - + +
726J ILE* 4.1 11.7 - - + -
747J VAL* 4.8 7.4 - - - -
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Residues in contact with ALA 649 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644J LEU* 3.6 26.5 - - + -
645J PRO 2.8 22.0 + - - +
648J MET* 1.3 70.8 - - - +
650J LEU* 1.3 61.0 + - - +
652J LEU* 3.2 6.4 + - - -
653J PHE* 2.9 40.9 + - + +
691J LEU* 4.3 3.4 - - + -
695J ILE* 5.0 2.2 - - + -
720J LEU* 3.6 25.1 - - + -
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Residues in contact with LEU 650 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646J LYS 2.9 15.4 + - - +
647J ARG* 3.3 6.5 + - - +
649J ALA* 1.3 75.6 - - - +
651J GLU* 1.3 65.1 + - + +
653J PHE* 3.0 5.5 + - - +
654J LYS* 2.9 37.6 + - + +
657J LEU* 3.7 27.5 - - + +
677J LEU* 4.4 17.3 - - + +
683J ILE* 3.6 29.6 - - + -
687J VAL* 4.3 8.3 - - + +
688J TRP* 3.7 16.6 - - + -
691J LEU* 3.7 17.2 - - + +
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Residues in contact with GLU 651 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007I ALA* 3.2 11.2 - - + +
1008I ARG* 3.2 26.7 + - - -
1009I SER* 2.8 40.3 + - - -
1010I THR 4.6 1.4 + - - +
1027I PHE* 4.1 20.0 - - + -
647J ARG 3.4 12.4 + - - +
648J MET* 4.2 2.7 - - - +
650J LEU* 1.3 82.4 - - + +
652J LEU* 1.3 60.7 + - - +
654J LYS* 3.6 31.7 + - + +
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Residues in contact with LEU 652 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007I ALA* 4.2 10.5 - - + +
1008I ARG 3.6 8.3 - - - +
1009I SER* 4.1 9.4 - - - -
625J TYR* 3.9 13.8 - - - -
626J SER* 3.3 42.8 - - - +
627J GLY 4.2 0.4 - - - +
644J LEU* 4.6 9.0 - - + -
648J MET* 2.9 28.0 + - + +
649J ALA 3.3 5.6 - - - +
650J LEU 3.1 0.2 - - - -
651J GLU* 1.3 79.8 + - - +
653J PHE* 1.3 75.2 + - + +
654J LYS 3.3 1.1 + - - -
655J PRO* 4.2 0.5 - - - +
656J PHE* 5.8 0.2 - - - -
700J VAL* 5.3 0.4 - - + -
747J VAL* 4.2 27.6 - - + +
749J VAL* 4.4 19.0 - - + +
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Residues in contact with PHE 653 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644J LEU* 4.1 22.9 - - + -
649J ALA* 2.9 31.2 + - + +
650J LEU 3.5 2.5 - - - +
652J LEU* 1.3 84.3 - - + +
654J LYS* 1.3 53.2 + - - +
655J PRO* 3.3 5.6 - - - -
656J PHE* 2.7 53.7 + + + +
657J LEU* 2.9 8.8 + - - -
691J LEU* 4.1 13.9 - - + -
694J VAL* 5.2 8.7 - - + -
695J ILE* 4.7 24.9 - - + -
698J LYS* 5.6 13.0 - - + -
700J VAL* 3.6 27.4 - - + -
718J PRO* 4.5 8.3 - - + -
749J VAL* 4.0 18.8 - - + -
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Residues in contact with LYS 654 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009I SER* 4.2 7.7 + - - +
1010I THR 5.8 1.2 + - - -
1067I TYR* 5.9 0.9 - - + -
650J LEU* 2.9 27.6 + - + +
651J GLU* 3.6 43.1 + - + +
652J LEU 3.3 0.8 - - - -
653J PHE* 1.3 74.9 - - - +
655J PRO* 1.3 71.4 - - + +
657J LEU* 4.3 5.6 - - - -
658J LEU* 2.9 36.9 + - + +
674J ARG* 4.5 23.4 - - - +
677J LEU* 4.6 15.3 - - + -
678J GLU* 4.5 17.8 + - - +
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Residues in contact with PRO 655 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009I SER* 4.2 9.9 - - - -
1010I THR* 5.3 0.4 - - - +
1067I TYR* 3.9 21.3 - - + -
1070I ILE* 3.6 33.0 - - + +
1071I ILE* 3.5 31.4 - - + +
625J TYR* 3.5 31.6 - - + -
652J LEU 4.2 2.2 - - - +
653J PHE* 3.4 4.5 - - - -
654J LYS* 1.3 95.7 - - + +
656J PHE* 1.3 62.7 + - + +
658J LEU* 3.7 7.1 - - + +
659J LYS 3.7 3.6 + - - -
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Residues in contact with PHE 656 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070I ILE* 3.7 36.1 - - + -
625J TYR* 6.2 1.8 - + - -
652J LEU 5.8 0.4 - - - -
653J PHE* 2.7 41.4 + + + +
655J PRO* 1.3 72.9 - - + +
657J LEU* 1.3 65.3 + - - +
658J LEU 3.1 1.3 - - - -
659J LYS* 2.9 17.6 + - - +
660J LYS 3.0 9.4 + - - -
694J VAL* 3.7 32.7 - - + +
698J LYS* 3.3 34.3 - - + -
749J VAL* 4.9 7.2 - - + -
750J PRO 5.2 2.2 - - - -
751J LEU* 4.4 31.2 - - + -
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Residues in contact with LEU 657 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650J LEU* 3.7 24.7 - - + +
653J PHE 2.9 11.7 + - - +
654J LYS* 3.8 8.5 - - - +
656J PHE* 1.3 76.6 - - - +
658J LEU* 1.3 57.7 + - - +
660J LYS* 3.2 0.6 + - + -
661J MET* 2.9 55.6 + - + +
677J LEU* 3.7 24.5 - - + -
687J VAL* 4.1 7.4 - - + +
690J ALA* 3.9 9.9 - - + +
691J LEU* 3.6 52.5 - - + +
694J VAL* 4.0 7.3 - - + +
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Residues in contact with LEU 658 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067I TYR* 5.0 5.2 - - - +
1071I ILE* 4.5 9.0 - - + -
654J LYS* 2.9 36.1 + - + +
655J PRO* 3.7 8.1 - - + +
657J LEU* 1.3 77.4 - - - +
659J LYS* 1.3 56.8 + - - +
661J MET* 3.4 6.4 + - - +
662J GLU* 2.9 26.0 + - - +
670J VAL* 3.0 53.5 - - + +
673J ALA* 3.8 6.4 - - + +
674J ARG* 3.3 26.9 - - + +
677J LEU* 3.7 28.3 - - + -
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Residues in contact with LYS 659 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070I ILE 3.4 20.6 - - - +
1071I ILE* 3.2 27.3 + - - +
1072I LYS* 3.8 20.0 + - - +
1073I GLY* 3.6 12.8 - - - +
655J PRO 3.7 2.0 + - - +
656J PHE* 2.9 11.0 + - + +
658J LEU* 1.3 78.6 - - - +
660J LYS* 1.3 59.7 + - + +
662J GLU* 3.0 28.4 + - - +
663J GLU* 2.9 54.9 + - - +
694J VAL* 5.6 2.2 - - + -
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Residues in contact with LYS 660 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656J PHE 3.0 5.7 + - - -
657J LEU* 3.8 4.5 - - - +
659J LYS* 1.3 77.2 - - + +
661J MET* 1.3 58.8 + - - +
662J GLU 3.3 0.2 - - - -
663J GLU* 3.3 28.2 + - + +
664J LYS* 3.2 32.6 + - + +
690J ALA* 3.6 27.9 - - + +
693J GLU* 3.6 40.0 + - + +
694J VAL* 3.6 34.8 - - + +
58K PRO* 3.9 23.4 - - - +
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Residues in contact with MET 661 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657J LEU* 2.9 53.4 + - + +
658J LEU 3.7 1.1 - - - +
660J LYS* 1.3 75.8 - - - +
662J GLU* 1.3 59.7 + - - +
664J LYS 3.9 1.1 + - - -
665J ALA 2.8 28.4 - - - +
666J PHE* 3.3 52.1 - - + +
667J ALA* 3.9 2.1 - - - +
673J ALA* 3.6 36.1 - - + +
676J MET* 4.7 7.4 - - + -
677J LEU* 3.6 34.8 - - + -
687J VAL* 4.1 4.0 - - + -
690J ALA* 4.6 0.7 - - + -
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Residues in contact with GLU 662 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658J LEU 2.9 13.7 + - - +
659J LYS* 3.1 34.1 - - - +
661J MET* 1.3 80.4 - - - +
663J GLU* 1.3 66.4 + - + +
665J ALA* 4.1 6.5 + - - +
667J ALA 4.7 4.9 - - - +
668J PRO 3.6 14.0 - - - +
669J ASN* 3.6 27.6 - - - +
670J VAL* 3.7 19.5 + - + +
432L LYS* 5.1 2.4 + - - -
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Residues in contact with GLU 663 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659J LYS* 2.9 48.1 + - + +
660J LYS* 3.3 33.4 + - + +
662J GLU* 1.3 79.9 - - + +
664J LYS* 1.3 59.1 + - + +
665J ALA 3.1 6.2 + - - -
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Residues in contact with LYS 664 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660J LYS* 3.2 19.4 + - + +
661J MET 3.9 2.0 + - - -
662J GLU 3.4 0.4 - - - -
663J GLU* 1.3 76.5 - - + +
665J ALA* 1.3 69.0 + - + +
666J PHE* 3.0 39.2 + - - -
686J GLU* 3.1 32.8 + - - +
689J ASP* 4.4 5.5 - - - +
690J ALA* 3.5 17.6 - - + +
693J GLU* 3.5 28.7 + - - +
52K GLU* 4.1 20.1 + - - +
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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
------------------------------------------------------------
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