Contacts of the helix formed by residues 646 - 663 (chain A) in PDB entry 3I5G
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 THR 646 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A GLU* 3.9 14.9 - - + +
540A CYS* 4.6 11.9 - - + -
600A ASN* 3.1 41.7 - - + +
601A LYS* 4.2 4.5 - - + -
602A ASP* 4.0 7.8 + - - -
644A PHE 5.5 0.4 - - - +
645A GLN* 1.3 91.7 + - - +
647A ILE* 1.3 65.6 + - - +
648A SER 4.1 0.9 - - - -
649A SER* 3.0 33.3 + - - -
650A VAL* 3.2 14.4 - - - +
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Residues in contact with ILE 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 5.2 9.4 - - + +
275A SER* 3.1 38.1 - - - +
431A LYS* 4.2 20.4 - - + +
475A PHE* 3.8 18.6 - - + -
479A CYS* 5.2 5.8 - - - -
599A LYS 3.0 25.4 - - - +
600A ASN* 3.1 13.2 + - - +
602A ASP* 3.9 17.9 - - + +
646A THR* 1.3 71.2 - - - +
648A SER* 1.3 61.7 + - - +
650A VAL* 3.3 6.1 + - - +
651A HIS* 2.9 28.9 + - + +
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Residues in contact with SER 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A PHE* 3.9 15.0 - - - -
479A CYS* 5.6 0.9 - - - -
533A LEU* 4.0 23.3 + - - +
536A LEU* 4.9 0.9 - - - -
537A GLU* 2.8 27.5 + - - +
600A ASN* 2.9 29.9 + - - -
646A THR* 4.0 0.2 + - - -
647A ILE* 1.3 74.9 - - - +
649A SER* 1.3 66.7 + - - +
651A HIS* 3.7 7.0 - - - +
652A LYS* 3.0 31.9 + - - +
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Residues in contact with SER 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A GLU* 4.0 9.9 - - - -
645A GLN* 3.9 13.7 - - - +
646A THR* 3.0 31.1 + - - -
647A ILE 3.3 0.4 - - - -
648A SER* 1.3 81.8 + - - +
650A VAL* 1.3 66.5 + - - +
652A LYS* 3.7 16.0 + - - +
653A GLU* 3.3 21.7 + - - +
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Residues in contact with VAL 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 4.6 27.8 - - - +
602A ASP* 5.0 2.0 - - - +
645A GLN* 5.4 3.8 - - + -
646A THR 3.2 19.4 + - - +
647A ILE* 3.8 5.6 - - - +
648A SER 3.2 0.2 - - - -
649A SER* 1.3 81.0 + - - +
651A HIS* 1.3 64.4 + - - +
653A GLU* 3.3 13.7 + - + +
654A SER* 3.0 26.0 + - - -
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Residues in contact with HIS 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.5 22.9 - - + +
479A CYS* 3.0 56.9 + - + +
480A ILE* 4.9 2.2 - - + -
482A TYR* 4.1 12.4 - + - -
483A THR* 2.9 23.2 + - - -
533A LEU* 6.1 1.6 - - + -
647A ILE* 2.9 20.0 + - + +
648A SER* 3.3 8.9 + - - +
650A VAL* 1.3 75.7 - - - +
652A LYS* 1.3 59.4 + - + +
654A SER* 3.1 2.5 + - - -
655A LEU* 2.8 37.7 + - + +
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Residues in contact with LYS 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A TYR* 4.0 22.2 - - + +
527A GLU* 4.7 17.7 + - + +
533A LEU* 3.8 31.5 - - + +
534A SER* 5.0 2.0 - - - +
537A GLU* 2.5 35.1 + - - -
648A SER 3.0 19.4 + - - +
649A SER* 3.7 11.7 - - - +
651A HIS* 1.3 78.8 - - - +
653A GLU* 1.3 51.5 - - - +
655A LEU* 3.7 5.2 - - - +
656A ASN* 2.7 49.3 + - - +
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Residues in contact with GLU 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A SER 3.3 11.6 + - - +
650A VAL* 3.3 17.2 + - + +
651A HIS 3.2 0.2 - - - -
652A LYS* 1.3 81.1 - - - +
654A SER* 1.3 61.9 + - - +
656A ASN* 3.3 9.4 + - - +
657A LYS* 3.1 22.5 + - - +
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Residues in contact with SER 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A TYR* 3.7 13.0 - - - +
271A LEU* 3.0 37.5 + - - -
650A VAL* 3.0 19.3 + - - -
651A HIS* 3.8 2.9 - - - -
653A GLU* 1.3 74.2 - - - +
655A LEU* 1.3 60.6 - - - +
657A LYS* 3.1 7.1 + - - +
658A LEU* 2.8 28.9 + - - +
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Residues in contact with LEU 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 4.0 6.2 - - + +
482A TYR* 3.9 22.4 - - + -
483A THR* 3.5 46.7 - - + +
486A ARG* 3.7 29.2 - - - +
651A HIS* 2.8 22.4 + - + +
652A LYS* 3.8 4.7 - - - +
654A SER* 1.3 73.7 - - - +
656A ASN* 1.3 66.6 + - - +
658A LEU* 3.3 8.5 + - + +
659A MET* 3.1 49.0 + - + +
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Residues in contact with ASN 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A TYR* 5.0 1.0 + - - -
486A ARG* 2.7 35.7 + - - +
527A GLU* 4.7 3.6 - - - +
652A LYS* 2.7 39.8 + - - +
653A GLU* 3.7 9.1 - - - +
654A SER 3.2 0.4 - - - -
655A LEU* 1.3 75.1 - - - +
657A LYS* 1.3 56.8 + - - +
659A MET* 3.7 2.4 - - - +
660A LYS* 3.0 27.3 + - - +
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Residues in contact with LYS 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU* 5.4 5.8 + - - +
270A TYR* 4.2 16.2 - - + -
653A GLU* 3.1 14.1 + - + +
654A SER* 3.1 9.6 + - - +
656A ASN* 1.3 75.0 - - - +
658A LEU* 1.3 69.4 + - - +
660A LYS* 3.2 6.9 + - + +
661A ASN* 3.1 44.2 + - - +
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Residues in contact with LEU 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A PHE* 5.5 3.1 - - + -
270A TYR* 3.5 45.9 - - + -
271A LEU* 4.3 10.8 - - + -
462A LEU* 4.4 23.6 - - + -
464A ILE* 3.7 28.7 - - + -
483A THR* 5.0 0.7 - - + -
487A LEU* 4.5 2.0 - - + -
654A SER 2.8 19.5 + - - +
655A LEU* 3.8 8.3 - - + +
657A LYS* 1.3 70.0 - - - +
659A MET* 1.3 80.2 + - + +
661A ASN* 2.9 19.7 + - + +
662A LEU* 3.0 20.7 + - + +
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Residues in contact with MET 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ARG* 3.8 54.7 - - + +
487A LEU* 3.2 33.7 - - + -
490A PHE* 4.8 1.8 - - - -
655A LEU* 3.1 36.0 + - + +
656A ASN 3.7 3.4 - - - +
658A LEU* 1.3 89.5 - - + +
660A LYS* 1.3 63.5 + - - +
661A ASN 2.8 6.1 + - - -
662A LEU* 3.0 23.3 + - + +
663A TYR* 3.1 38.4 + - + -
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Residues in contact with LYS 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A ASN 3.0 18.7 + - - +
657A LYS* 3.2 9.2 + - + +
659A MET* 1.3 75.5 - - - +
661A ASN* 1.3 70.7 + - - +
663A TYR* 4.3 5.3 + - - +
664A SER* 3.3 31.8 + - - -
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Residues in contact with ASN 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A PHE* 5.2 9.6 - - + -
268A GLU* 4.0 10.3 - - - +
270A TYR* 2.8 28.0 + - - +
458A PHE* 5.9 0.2 - - - -
657A LYS* 3.2 28.9 + - - +
658A LEU* 2.9 9.1 + - + +
659A MET 2.8 1.6 + - - -
660A LYS* 1.3 93.8 + - - +
662A LEU* 1.3 66.6 + - + +
663A TYR 3.4 0.4 - - - -
664A SER* 3.2 17.8 + - - -
665A THR* 3.4 12.8 - - - +
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Residues in contact with LEU 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A SER* 4.2 12.8 - - - +
173A LEU* 4.0 31.6 - - + -
251A PHE* 4.5 13.5 - - + -
462A LEU* 4.1 15.9 - - + -
487A LEU* 3.4 32.8 - - + -
490A PHE* 3.5 24.0 - - + -
658A LEU* 3.0 20.7 + - + +
659A MET* 3.0 21.9 + - + +
661A ASN* 1.3 72.2 - - + +
663A TYR* 1.3 57.1 + - - +
664A SER 2.9 11.5 + - - -
665A THR* 2.9 27.0 + - - +
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Residues in contact with TYR 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A ARG* 4.5 3.9 + - - -
489A GLN* 3.9 18.5 + - - +
490A PHE* 3.2 54.3 + + + -
493A HIS* 4.0 30.2 - + - +
659A MET* 3.1 42.0 + - + +
660A LYS* 4.5 4.9 - - - +
662A LEU* 1.3 74.6 - - - +
664A SER* 1.3 57.0 + - - +
665A THR 3.3 5.0 + - - +
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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
------------------------------------------------------------
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