Contacts of the helix formed by residues 607 - 625 (chain S) in PDB entry 5IJ7
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 607 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A CYS* 4.1 9.4 - - - -
261A THR* 3.0 28.2 + - - +
262A PRO* 3.6 3.3 - - + +
263A ASN* 3.1 34.5 + - + +
605S ASP 4.1 0.4 + - - -
606S VAL* 1.3 75.4 - - - +
608S GLU* 1.3 59.9 + - - +
609S GLY 2.8 28.5 - - - +
610S GLU* 2.9 38.3 + - - +
611S LYS* 3.0 28.0 + - - +
655S ASN* 4.8 0.2 - - - +
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Residues in contact with GLU 608 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN* 5.2 3.8 + - - +
601S GLU* 2.9 28.5 - - - +
606S VAL 4.4 2.8 - - - +
607S ASN* 1.3 74.4 - - - +
609S GLY* 1.3 59.9 + - - +
611S LYS* 3.3 24.9 + - + +
612S GLU* 3.4 23.4 + - - +
652S LEU* 4.6 0.9 - - - +
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Residues in contact with GLY 609 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN* 3.9 13.7 - - - +
607S ASN* 2.8 17.3 - - - +
608S GLU* 1.3 70.0 - - - +
610S GLU* 1.3 60.3 + - - -
612S GLU 3.5 1.0 + - - -
613S VAL* 3.4 15.6 + - - +
652S LEU* 3.4 26.4 - - - +
655S ASN* 3.5 21.8 - - - -
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Residues in contact with GLU 610 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR* 4.9 7.0 - - - +
276A GLN 5.0 2.3 - - - +
277A SER 3.5 20.8 - - - +
280A SER* 2.8 36.1 + - - -
281A PHE* 3.6 28.6 - - + -
605S ASP 4.8 0.5 - - - +
606S VAL* 3.6 9.4 - - + +
607S ASN* 2.9 44.5 + - - +
609S GLY* 1.3 70.8 - - - +
611S LYS* 1.3 65.6 + - - +
613S VAL* 3.3 4.0 + - - +
614S MET* 3.1 31.6 + - + +
655S ASN* 3.7 9.4 + - - +
658S LEU* 5.3 0.9 - - + +
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Residues in contact with LYS 611 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600S ILE* 3.4 34.2 - - + +
601S GLU* 3.0 40.2 + - - +
603S PHE 2.9 30.4 + - - -
606S VAL* 3.3 27.3 + - + +
607S ASN 3.0 16.4 + - - +
608S GLU* 3.3 30.3 + - - +
610S GLU* 1.3 75.0 - - - +
612S GLU* 1.4 58.1 + - - +
614S MET* 3.3 4.7 + - - +
615S LYS* 3.0 36.2 + - - +
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Residues in contact with GLU 612 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601S GLU* 5.1 0.3 - - - +
608S GLU 3.4 15.1 + - - +
609S GLY 3.5 0.2 + - - -
610S GLU 3.4 0.6 - - - -
611S LYS* 1.4 76.0 - - - +
613S VAL* 1.3 65.1 + - - +
615S LYS* 3.6 29.3 + - - +
616S LEU* 3.2 41.3 + - + +
650S LYS* 3.7 34.1 + - + -
652S LEU* 3.7 23.6 - - + -
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Residues in contact with VAL 613 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PHE* 4.4 6.3 - - + -
292A TYR* 5.8 0.4 - - + -
609S GLY 3.4 13.1 + - - +
610S GLU 3.3 7.0 + - - +
611S LYS 3.3 0.6 - - - -
612S GLU* 1.3 75.2 - - - +
614S MET* 1.4 53.9 + - - +
616S LEU* 3.4 7.3 + - - +
617S TRP* 2.9 33.6 + - + +
639S PHE* 4.5 4.0 - - + -
647S ILE* 4.3 10.1 - - + -
652S LEU* 3.7 25.8 - - + +
655S ASN* 3.7 20.2 - - + +
656S PHE* 4.0 14.1 - - + +
659S HIS* 3.9 33.9 - - + +
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Residues in contact with MET 614 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A SER* 3.4 41.7 - - - +
281A PHE* 3.8 13.5 - - + +
284A LEU* 3.7 24.5 - - + -
292A TYR* 3.6 51.6 - - + -
600S ILE* 4.2 13.0 - - + -
606S VAL* 4.5 6.3 - - + -
610S GLU* 3.1 23.9 + - + +
611S LYS 3.5 4.9 - - - +
613S VAL* 1.4 73.1 - - - +
615S LYS* 1.3 59.4 + - - +
617S TRP* 3.4 1.2 + - - +
618S ASN* 3.0 37.3 + - - +
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Residues in contact with LYS 615 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596S THR* 5.3 1.1 - - - +
597S ILE* 3.4 51.0 + - + +
600S ILE* 3.9 21.3 - - + -
601S GLU* 2.8 42.5 + - - +
611S LYS* 3.0 19.7 + - - +
612S GLU* 3.6 36.0 + - - +
614S MET* 1.3 73.9 - - - +
616S LEU* 1.4 59.8 + - + +
618S ASN* 3.4 5.7 + - - +
619S LEU* 3.0 37.9 + - + +
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Residues in contact with LEU 616 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612S GLU* 3.2 35.0 + - + +
613S VAL 3.6 3.8 - - - +
615S LYS* 1.4 77.2 - - + +
617S TRP* 1.3 64.8 + - - +
619S LEU* 3.5 15.2 + - + +
620S HIS* 3.1 22.9 + - - +
639S PHE* 3.4 14.8 - - + -
643S TYR* 3.7 27.2 - - + -
646S LYS* 4.3 21.1 - - + -
647S ILE* 3.8 25.1 - - + -
650S LYS* 5.0 4.9 - - + -
652S LEU* 4.5 10.5 - - + -
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Residues in contact with TRP 617 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PHE* 3.8 8.3 - + - -
290A PHE 2.9 26.6 + - - -
292A TYR* 3.8 28.5 - + + -
613S VAL* 2.9 18.0 + - + +
614S MET 3.8 3.8 - - - +
616S LEU* 1.3 73.8 - - - +
618S ASN* 1.3 62.4 + - - +
620S HIS* 3.2 11.4 + + - +
621S VAL* 2.9 39.6 + - + +
632S MET* 3.3 17.3 - - + -
635S ALA* 3.9 23.1 - - + -
636S CYS* 3.9 9.0 - - - -
639S PHE* 3.7 43.0 - + + -
659S HIS* 3.4 29.8 - + + +
663S MET* 3.3 22.2 - - + -
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Residues in contact with ASN 618 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LYS* 3.4 16.6 - - - +
292A TYR* 2.8 52.9 + - - +
293A ASP 5.0 0.8 + - - -
294A CYS* 5.9 0.2 - - - +
295A PHE* 6.0 0.4 - - - -
596S THR* 2.9 31.2 + - + +
600S ILE* 4.2 5.7 - - - +
614S MET 3.0 21.1 + - - +
615S LYS* 3.6 5.8 - - - +
617S TRP* 1.3 75.4 - - - +
619S LEU* 1.3 56.8 + - - +
621S VAL* 3.4 5.9 + - - +
622S MET* 2.9 39.7 + - - +
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Residues in contact with LEU 619 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593S ARG* 3.7 55.7 - - + +
596S THR* 4.2 6.7 - - + -
597S ILE* 3.7 26.2 - - + -
615S LYS* 3.0 29.8 + - + +
616S LEU* 3.8 17.9 - - + +
617S TRP 3.3 0.2 - - - -
618S ASN* 1.3 74.8 - - - +
620S HIS* 1.3 55.9 + - - +
622S MET* 3.8 4.3 + - - +
623S LYS* 3.2 27.9 + - - +
643S TYR* 3.9 15.5 + - + +
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Residues in contact with HIS 620 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616S LEU 3.1 13.4 + - - +
617S TRP* 3.2 21.5 + + - +
619S LEU* 1.3 74.8 - - - +
621S VAL* 1.4 64.0 + - + +
623S LYS* 3.3 4.3 + - - +
624S HIS* 3.1 59.3 + + - +
626S PHE* 3.7 16.0 - + - -
635S ALA 2.8 24.9 + - - -
638S LEU* 3.6 14.4 - - + -
639S PHE* 3.6 34.3 + + + -
642S ASN* 4.4 0.6 + - - -
643S TYR* 3.6 26.3 + - + -
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Residues in contact with VAL 621 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A CYS 4.0 6.1 - - - +
290A PHE* 3.5 14.4 - - + +
291A LYS* 3.8 31.7 + - + +
617S TRP* 2.9 58.2 + - + +
618S ASN 4.0 3.4 - - - +
620S HIS* 1.4 73.8 - - + +
622S MET* 1.4 53.4 + - - +
624S HIS 3.5 0.3 + - - -
625S GLY* 2.8 33.3 + - - -
626S PHE* 3.7 31.5 + - + +
632S MET* 5.4 0.2 - - + -
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Residues in contact with MET 622 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LYS* 3.9 25.6 - - + +
295A PHE* 4.9 7.0 - - + -
587S LYS* 4.4 6.4 - - - +
588S ASP* 3.5 25.4 - - + +
592S LEU* 3.5 21.8 - - + +
593S ARG* 3.5 41.5 - - + +
596S THR* 3.8 23.1 - - - -
618S ASN* 2.9 25.4 + - - +
619S LEU* 4.0 6.7 - - - +
621S VAL* 1.4 73.3 - - - +
623S LYS* 1.4 64.5 + - - +
624S HIS 3.7 0.2 + - - -
625S GLY* 3.9 6.2 + - - -
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Residues in contact with LYS 623 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587S LYS* 3.4 22.5 + - - +
588S ASP* 3.8 32.6 + - - +
593S ARG* 5.1 11.8 - - - +
619S LEU 3.2 20.7 + - - +
620S HIS* 3.3 7.6 + - - +
622S MET* 1.4 76.8 - - - +
624S HIS* 1.4 76.2 + - + +
643S TYR* 5.2 7.4 - - - +
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Residues in contact with HIS 624 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587S LYS* 3.3 15.2 + - - +
620S HIS* 3.1 47.8 + + - -
623S LYS* 1.4 94.0 - - + +
625S GLY* 1.3 64.9 + - - +
626S PHE* 3.4 31.9 + + + -
638S LEU* 3.6 22.7 - - + +
642S ASN* 3.8 13.0 + - - -
643S TYR* 5.8 0.9 - + - -
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Residues in contact with GLY 625 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LYS* 6.2 1.3 - - - -
587S LYS* 4.0 12.2 + - - +
621S VAL* 2.8 15.2 + - - -
622S MET* 3.9 4.6 + - - -
623S LYS 3.6 2.8 - - - -
624S HIS* 1.3 77.4 - - - +
626S PHE* 1.4 63.9 + - - -
627S ILE* 3.4 16.9 + - - +
631S GLN* 4.8 0.5 + - - +
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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