Contacts of the helix formed by residues 652 - 664 (chain M) in PDB entry 6C23
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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265K ASP* 3.6 13.2 - - - +
609M GLY* 4.1 20.6 - - - +
612M GLU* 4.2 19.5 - - + -
613M VAL* 4.8 11.4 - - + +
616M LEU* 5.0 5.2 - - + -
647M ILE* 3.2 31.2 + - + +
650M LYS* 3.4 40.2 - - + -
651M ASN* 1.3 70.9 - - - +
653M CYS* 1.3 63.8 + - - +
654M ARG 3.3 2.7 - - - -
655M ASN* 3.5 28.3 - - + +
656M PHE* 2.9 25.1 + - + +
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Residues in contact with CYS 653 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647M ILE* 6.0 0.9 - - - -
651M ASN* 3.5 11.8 + - - -
652M LEU* 1.3 81.7 - - - +
654M ARG* 1.3 58.0 + - - +
656M PHE* 3.8 5.1 - - - +
657M MET* 2.9 31.9 + - - +
681M LEU* 4.9 18.4 - - + -
682M ARG* 3.5 34.3 - - - +
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Residues in contact with ARG 654 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264K ILE* 3.1 51.5 - - + +
265K ASP* 4.0 5.6 - - - +
652M LEU 3.3 0.2 - - - -
653M CYS* 1.3 80.2 - - - +
655M ASN* 1.3 58.3 + - - +
657M MET* 3.3 5.8 + - - +
658M LEU* 2.9 30.8 + - - +
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Residues in contact with ASN 655 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263K ASN* 4.0 12.4 + - - +
264K ILE* 4.5 16.5 - - - +
265K ASP* 3.5 27.0 - - - +
281K PHE* 4.3 5.8 - - + -
607M ASN* 4.8 3.6 - - - +
609M GLY* 4.1 11.6 - - - +
610M GLU* 4.1 13.9 - - - +
613M VAL* 4.4 17.7 - - + +
652M LEU* 3.5 24.7 + - + +
653M CYS 3.4 0.4 - - - -
654M ARG* 1.3 76.4 - - - +
656M PHE* 1.3 58.3 + - - +
658M LEU* 3.2 8.9 + - - +
659M HIS* 2.9 28.6 + - - +
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Residues in contact with PHE 656 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613M VAL* 4.4 16.4 - - + -
617M TRP* 5.8 0.7 - + - -
636M CYS* 4.8 3.6 - - + -
639M PHE* 3.5 35.9 - + - -
640M VAL* 3.3 33.2 - - + -
647M ILE* 4.5 16.2 - - + -
652M LEU* 2.9 19.6 + - + +
653M CYS* 3.8 4.5 - - - +
655M ASN* 1.3 77.7 - - - +
657M MET* 1.3 59.0 + - + +
659M HIS* 3.2 13.5 + + + +
660M LEU* 2.9 66.5 + - + +
677M ALA* 5.0 4.7 - - + -
678M VAL* 5.4 6.1 - - + -
681M LEU* 5.1 12.8 - - + -
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Residues in contact with MET 657 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443K LEU* 6.4 2.0 - - + -
457K LEU* 6.4 1.6 - - + -
653M CYS 2.9 18.1 + - - +
654M ARG* 3.7 5.8 - - - +
656M PHE* 1.3 79.2 - - + +
658M LEU* 1.3 55.9 + - - +
660M LEU* 3.2 13.8 + - - +
661M VAL* 2.9 35.9 + - + +
674M ILE* 5.4 2.9 - - + +
678M VAL* 5.2 11.2 - - + -
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Residues in contact with LEU 658 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264K ILE* 3.3 29.8 - - + -
277K SER* 3.5 30.3 - - - +
278K LEU* 3.2 30.3 - - + +
281K PHE* 3.3 26.5 - - + -
439K MET* 6.5 0.4 - - - -
442K VAL* 5.7 5.6 - - + -
610M GLU* 5.5 1.8 - - + +
654M ARG 2.9 16.0 + - - +
655M ASN* 3.4 8.5 - - - +
657M MET* 1.3 77.1 - - - +
659M HIS* 1.3 55.1 + - - +
661M VAL* 3.2 10.8 + - + +
662M SER* 2.9 25.1 + - - -
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Residues in contact with HIS 659 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281K PHE* 3.5 35.2 - + + -
285K PHE* 4.7 12.3 - + - -
292K TYR* 5.7 1.3 - - + -
613M VAL* 4.7 13.2 - - + +
614M MET* 5.2 14.1 - - + +
617M TRP* 3.6 54.4 - + + -
636M CYS* 6.5 0.2 - - - -
639M PHE* 6.3 0.4 - + - -
655M ASN 2.9 10.8 + - - +
656M PHE* 3.4 17.5 - + + +
658M LEU* 1.3 74.9 - - - +
660M LEU* 1.3 65.1 + - + +
662M SER* 3.2 5.3 + - - -
663M MET* 2.9 41.0 + - + +
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Residues in contact with LEU 660 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636M CYS* 4.1 30.5 - - + -
656M PHE* 2.9 58.2 + - + +
657M MET* 3.2 9.2 + - - +
659M HIS* 1.3 80.5 - - + +
661M VAL* 1.3 61.9 + - - +
663M MET* 3.1 12.6 + - + +
664M HIS* 3.0 17.7 + - - +
669M ILE* 3.7 9.5 - - + +
674M ILE* 4.2 25.8 - - + +
677M ALA* 4.4 10.8 - - + -
678M VAL* 4.3 20.0 - - + -
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Residues in contact with VAL 661 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278K LEU* 4.3 17.9 - - + -
442K VAL* 4.4 20.0 - - + +
443K LEU* 4.5 22.9 - - + -
446K THR* 4.8 22.0 - - + -
447K TYR* 5.2 2.7 - - + +
657M MET* 2.9 23.1 + - + +
658M LEU* 3.2 11.0 + - - +
660M LEU* 1.3 77.2 - - + +
662M SER* 1.3 54.8 + - - +
664M HIS* 2.7 37.2 + - - +
665M ASP* 4.1 4.0 - - - +
674M ILE* 5.4 9.0 - - + -
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Residues in contact with SER 662 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278K LEU* 4.3 9.5 - - - +
281K PHE* 3.3 45.0 + - - +
282K HIS* 4.3 1.2 + - - -
285K PHE* 5.5 2.1 - - - +
658M LEU 2.9 12.2 + - - -
659M HIS* 3.5 10.3 - - - -
661M VAL* 1.3 77.5 - - - +
663M MET* 1.3 60.7 + - - +
665M ASP* 3.2 32.5 + - - +
666M PHE* 4.0 11.4 - - - -
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Residues in contact with MET 663 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285K PHE* 3.7 33.2 - - + -
617M TRP* 4.2 22.2 - - + -
632M MET* 4.3 21.8 - - + -
636M CYS* 4.5 15.5 - - - -
659M HIS* 2.9 32.0 + - + +
660M LEU* 3.2 12.6 - - - +
662M SER* 1.3 76.1 - - - +
664M HIS* 1.3 55.3 + - - +
665M ASP 3.2 4.1 + - - -
666M PHE* 3.9 7.1 + - - -
668M LEU* 3.8 41.0 + - + +
669M ILE* 3.3 23.6 - - + +
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Residues in contact with HIS 664 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446K THR* 3.4 34.3 + - - +
660M LEU 3.0 9.2 + - - +
661M VAL* 2.7 23.0 + - - +
663M MET* 1.3 69.4 - - - +
665M ASP* 1.3 63.6 + - - +
667M ASN* 4.6 17.4 + - - +
669M ILE* 3.1 32.2 + - + +
670M SER* 3.5 20.0 - - - -
671M ILE* 3.8 11.7 + - + +
674M ILE* 3.9 13.0 - - + -
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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
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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