Contacts of the helix formed by residues 652 - 666 (chain T) 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 LEU 652 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263B ASN* 5.4 0.7 - - - +
265B ASP* 3.3 12.1 - - - -
608T GLU 4.6 0.9 - - - +
609T GLY* 3.4 37.9 - - - +
612T GLU* 3.7 27.8 - - + -
613T VAL* 3.7 13.0 - - + +
616T LEU* 4.5 4.7 - - + -
647T ILE* 2.9 32.1 + - + +
650T LYS* 3.7 31.4 - - + +
651T ASN* 1.3 80.8 - - - +
653T CYS* 1.3 57.8 + - - +
655T ASN* 4.5 1.1 - - - +
656T PHE* 3.0 30.5 + - - +
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Residues in contact with CYS 653 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP* 3.5 6.5 + - - +
647T ILE* 3.9 7.9 - - - -
648T ILE* 4.0 33.2 - - - -
651T ASN* 3.7 4.0 - - - +
652T LEU* 1.3 76.6 - - - +
654T ARG* 1.4 59.3 + - + +
656T PHE* 3.7 8.1 - - - +
657T MET* 3.4 21.7 + - - +
681T LEU* 3.9 23.5 - - + +
685T GLN* 4.0 16.8 - - - -
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Residues in contact with ARG 654 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 2.9 46.9 + - + -
265B ASP* 3.1 46.7 + - - +
435B ALA* 4.2 14.0 - - - +
439B MET* 3.6 11.6 - - + +
651T ASN* 3.7 10.5 + - - -
653T CYS* 1.4 74.3 - - + +
655T ASN* 1.3 60.0 + - - +
656T PHE 3.2 2.0 - - - -
657T MET* 3.1 13.3 + - - +
658T LEU* 3.0 29.6 + - - +
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Residues in contact with ASN 655 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASN* 3.6 16.3 - - - +
264B ILE* 3.5 16.2 + - - +
265B ASP* 2.8 31.3 + - - +
281B PHE* 3.3 16.0 - - + -
607T ASN* 4.8 0.2 - - - +
609T GLY* 3.5 29.7 - - - +
610T GLU* 3.7 20.6 + - - +
613T VAL* 3.7 22.2 - - + +
652T LEU* 3.5 4.5 + - - +
654T ARG* 1.3 69.4 - - - +
656T PHE* 1.4 58.4 + - - +
658T LEU* 3.3 9.4 + - - +
659T HIS* 3.1 21.0 + - - +
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Residues in contact with PHE 656 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613T VAL* 4.0 9.8 - - + +
617T TRP* 6.0 0.2 - + - -
636T CYS* 4.8 2.2 - - + -
639T PHE* 3.5 37.5 - + + -
640T VAL* 3.6 31.6 - - + -
647T ILE* 4.2 15.5 - - + -
652T LEU 3.0 19.2 + - - +
653T CYS 3.7 4.9 - - - +
655T ASN* 1.4 74.5 - - - +
657T MET* 1.4 60.0 + - + +
659T HIS* 3.2 14.5 + + + +
660T LEU* 3.0 59.3 + - + +
677T ALA* 4.3 7.4 - - + -
678T VAL* 5.1 3.1 - - + -
681T LEU* 3.7 30.5 - - + -
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Residues in contact with MET 657 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B MET* 3.4 35.2 - - + +
443B LEU* 3.6 11.7 - - + -
457B LEU* 3.4 61.7 - - + +
653T CYS 3.4 12.5 + - - +
654T ARG* 3.1 19.2 + - + +
656T PHE* 1.4 78.7 - - - +
658T LEU* 1.3 57.6 + - - +
660T LEU* 3.3 14.1 + - + +
661T VAL* 3.0 34.1 + - + +
674T ILE* 5.5 1.5 - - + +
678T VAL* 4.3 14.1 - - + -
682T ARG* 4.6 2.0 - - - -
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Residues in contact with LEU 658 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B ILE* 3.8 28.0 - - + -
277B SER* 3.5 28.9 - - - +
278B LEU* 3.3 19.0 - - + +
281B PHE* 3.8 18.6 - - + -
439B MET* 4.0 16.2 - - + -
442B VAL* 3.8 37.5 - - + -
610T GLU* 5.3 1.1 - - - +
654T ARG 3.0 13.3 + - - +
655T ASN* 3.4 13.0 - - - +
656T PHE 3.3 0.2 - - - -
657T MET* 1.3 73.1 - - - +
659T HIS* 1.3 59.8 + - - +
661T VAL* 3.5 2.4 + - - -
662T SER* 3.0 24.8 + - - -
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Residues in contact with HIS 659 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 3.7 22.8 - - + -
292B TYR* 2.8 34.1 - + - -
613T VAL* 3.9 13.1 - - + +
617T TRP* 3.4 40.0 + + + -
636T CYS* 4.8 3.8 - - - -
639T PHE* 5.2 0.6 - + - -
655T ASN 3.1 8.7 + - - +
656T PHE* 3.2 27.1 + + - +
658T LEU* 1.3 75.7 - - - +
660T LEU* 1.3 58.9 + - + +
662T SER* 3.3 3.7 + - - -
663T MET* 2.9 61.5 + - + +
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Residues in contact with LEU 660 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636T CYS* 4.1 20.0 - - + -
656T PHE* 3.0 53.3 + - + +
657T MET* 3.3 10.3 + - - +
659T HIS* 1.3 78.2 - - - +
661T VAL* 1.4 56.0 + - - +
663T MET* 3.4 2.5 + - - -
664T HIS* 3.1 22.5 + - - +
669T ILE* 3.2 32.1 - - + +
673T SER 4.7 0.9 - - - +
674T ILE* 3.9 18.3 - - + +
677T ALA* 4.0 21.3 - - + -
678T VAL* 3.9 23.8 - - + -
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Residues in contact with VAL 661 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 3.9 2.0 - - - +
278B LEU* 3.8 22.4 - - + -
439B MET* 5.8 0.2 - - - -
442B VAL* 3.7 32.8 - - + -
443B LEU* 5.1 10.8 - - + -
446B THR* 3.8 21.1 - - - +
447B TYR* 6.3 0.2 - - + -
657T MET* 3.0 27.7 + - + +
658T LEU* 4.3 0.9 - - + -
659T HIS 3.4 0.2 - - - -
660T LEU* 1.4 73.8 - - + +
662T SER* 1.4 57.1 + - - +
664T HIS* 3.1 4.6 + - - +
665T ASP* 2.8 37.0 + - - +
674T ILE* 4.0 18.8 - - + -
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Residues in contact with SER 662 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 4.3 2.0 - - - -
281B PHE* 3.6 24.2 + - - +
282B HIS* 3.5 19.7 - - - -
285B PHE* 5.1 0.7 - - - +
292B TYR* 4.4 4.9 + - - -
658T LEU 3.0 18.9 + - - -
659T HIS* 3.4 6.3 - - - -
661T VAL* 1.4 76.6 - - - +
663T MET* 1.4 57.0 + - - +
665T ASP* 3.1 15.1 + - - +
666T PHE* 2.9 45.4 + - - -
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Residues in contact with MET 663 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B PHE* 3.7 30.1 - - - -
617T TRP* 3.3 20.2 - - + -
632T MET* 3.7 7.0 - - + -
636T CYS* 3.5 16.2 - - - -
659T HIS* 2.9 51.3 + - + +
660T LEU* 3.5 10.1 - - - +
661T VAL 3.2 0.2 - - - -
662T SER* 1.4 73.6 + - - +
664T HIS* 1.3 60.2 + - - +
666T PHE* 3.4 6.8 + - - +
667T ASN 3.4 3.6 + - - -
668T LEU* 3.0 44.1 + - + +
669T ILE* 3.7 16.1 + - + -
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Residues in contact with HIS 664 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B ARG* 3.0 68.3 + - + +
446B THR* 3.6 32.3 + - + +
660T LEU 3.1 13.1 + - - +
661T VAL 3.3 7.0 - - - +
663T MET* 1.3 73.9 - - - +
665T ASP* 1.4 69.2 + - - +
667T ASN 3.1 5.5 + - - -
669T ILE* 3.3 19.0 + - + +
670T SER 4.1 0.2 - - - -
671T ILE* 3.5 37.5 + - + -
674T ILE* 3.8 15.9 - - + -
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Residues in contact with ASP 665 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ARG* 3.0 32.8 + - - -
278B LEU* 3.5 5.4 - - - +
282B HIS* 2.8 26.5 + - - +
305B THR 3.4 0.2 - - - +
306B TYR* 3.4 21.8 - - - +
307B LYS* 3.0 24.8 + - - +
308B ARG* 4.9 2.6 - - - +
445B GLY 5.5 0.9 - - - +
446B THR* 4.2 4.5 + - - -
661T VAL 2.8 21.0 + - - +
662T SER* 3.1 8.2 + - - +
664T HIS* 1.4 82.1 - - - +
666T PHE* 1.3 56.8 + - - +
667T ASN* 3.2 13.2 + - - -
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Residues in contact with PHE 666 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B PHE 4.0 3.4 - - - -
282B HIS* 3.5 25.1 - + - -
285B PHE* 3.6 39.3 - + + -
287B ARG* 3.7 39.5 + - + -
301B ALA* 4.1 9.9 - - + -
305B THR* 3.5 36.1 - - - +
306B TYR* 3.7 19.1 - + + -
662T SER* 2.9 43.0 + - - +
663T MET 3.8 5.8 - - - +
664T HIS 3.3 0.4 - - - -
665T ASP* 1.3 73.0 - - - +
667T ASN* 1.4 68.3 + - - +
668T LEU* 3.4 16.9 - - + +
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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