Contacts of the helix formed by residues 655 - 673 (chain A) in PDB entry 3H44
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 ASP 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599A LEU* 5.7 0.4 - - - +
652A PHE* 5.5 1.2 - - - -
653A GLU 3.6 3.2 + - - +
654A ILE* 1.3 73.9 - - - +
656A GLU* 1.3 66.3 + - - +
657A LYS* 2.8 17.4 + - - +
658A ARG* 2.8 47.6 + - + +
659A PHE* 3.1 21.3 + - - +
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Residues in contact with GLU 656 (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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654A ILE 3.6 4.6 + - - -
655A ASP* 1.3 73.7 + - - +
657A LYS* 1.3 68.4 + - + +
659A PHE* 3.5 5.7 + - - +
660A GLU* 3.0 44.8 + - + +
709A LEU* 3.4 36.4 - - + +
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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
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352A SER 5.4 2.2 + - - -
353A LYS 4.6 5.7 + - - -
354A GLY* 4.3 14.5 + - - +
382A GLU* 6.2 2.0 - - - +
655A ASP* 2.8 16.5 + - - +
656A GLU* 1.3 77.3 - - + +
658A ARG* 1.3 64.7 + - + +
660A GLU* 3.3 10.4 + - + +
661A ILE* 3.0 55.4 + - + +
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Residues in contact with ARG 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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351A LYS* 3.9 36.8 + - - +
354A GLY* 4.5 1.2 - - - -
356A VAL 4.4 2.6 + - - -
357A ASN* 3.3 27.8 + - - -
380A THR* 5.2 0.4 - - - +
599A LEU* 3.8 12.3 - - + -
602A ASP* 2.9 49.1 + - - +
655A ASP* 2.8 36.3 + - + +
657A LYS* 1.3 73.1 - - + +
659A PHE* 1.3 54.7 + - - +
661A ILE* 3.2 27.0 + - - +
662A ILE* 2.8 45.6 + - + +
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Residues in contact with PHE 659 (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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595A LEU* 5.2 5.6 - - + +
599A LEU* 3.5 16.0 - - + +
654A ILE* 3.9 13.5 - - + -
655A ASP 3.1 9.5 + - - +
656A GLU* 3.5 10.5 - - - +
658A ARG* 1.3 78.2 - - - +
660A GLU* 1.3 92.8 + - - +
662A ILE* 4.2 0.3 - - - +
663A LYS* 2.9 42.5 + - + +
707A VAL* 3.7 33.9 - - + -
708A THR* 3.7 4.9 - - - -
709A LEU* 3.6 43.3 - - + -
712A LEU* 4.2 24.2 - - + -
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Residues in contact with GLU 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 GLU* 3.0 33.4 + - + +
657A LYS* 3.3 14.8 + - + +
659A PHE* 1.3 100.6 - - - +
661A ILE* 1.3 58.9 + - + +
663A LYS* 3.6 14.6 + - - +
664A GLU* 3.0 29.0 + - - +
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Residues in contact with ILE 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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354A GLY* 4.0 19.1 - - - +
357A ASN* 3.6 36.1 - - - +
380A THR* 4.0 20.6 - - + -
657A LYS* 3.0 42.6 + - + +
658A ARG* 3.6 24.5 - - - +
660A GLU* 1.3 72.9 - - + +
662A ILE* 1.3 68.8 + - + +
664A GLU* 3.2 10.2 + - - +
665A ALA* 3.1 19.8 + - - +
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Residues in contact with ILE 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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357A ASN* 5.7 2.5 - - - +
594A TYR* 5.4 0.9 - - + -
595A LEU* 3.6 22.9 - - + -
598A GLU* 4.0 24.7 - - + +
599A LEU* 3.6 27.6 - - + +
602A ASP* 4.1 30.3 - - + +
658A ARG* 2.8 38.5 + - - +
659A PHE 4.2 2.0 - - - +
661A ILE* 1.3 74.0 - - + +
663A LYS* 1.3 58.5 + - - +
665A ALA* 2.9 10.8 + - + +
666A TYR* 2.8 26.5 + - + +
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Residues in contact with LYS 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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595A LEU* 4.2 17.5 - - + -
659A PHE* 2.9 43.0 + - + +
660A GLU* 3.6 13.2 + - - +
662A ILE* 1.3 77.2 - - - +
664A GLU* 1.3 63.5 + - - +
666A TYR* 3.2 2.4 + - - +
667A MET* 3.1 41.6 + - + +
704A LEU* 3.4 39.9 + - + +
705A ASP* 3.9 11.9 + - - +
707A VAL* 3.3 18.9 + - + +
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Residues in contact with GLU 664 (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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311A ARG* 2.5 40.5 + - - -
381A GLU* 3.8 27.7 - - + +
660A GLU 3.0 15.2 + - - +
661A ILE* 3.5 11.7 - - - +
663A LYS* 1.3 76.1 - - - +
665A ALA* 1.3 62.7 + - - +
667A MET* 3.4 16.0 + - + +
668A ARG* 3.0 45.4 + - - +
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Residues in contact with ALA 665 (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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357A ASN* 5.3 8.5 - - - +
661A ILE 3.1 10.7 + - - +
662A ILE* 2.9 13.9 + - + +
664A GLU* 1.3 74.3 + - - +
666A TYR* 1.3 60.7 + - - +
668A ARG* 3.1 29.7 + - - +
669A SER* 2.8 30.8 + - - -
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Residues in contact with TYR 666 (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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590A SER 5.2 0.5 + - - -
591A ASN* 2.9 37.6 + - + -
594A TYR* 3.2 47.7 - + + +
595A LEU* 3.9 18.4 - - + -
662A ILE* 2.8 12.7 + - + +
663A LYS 3.2 7.2 + - - +
665A ALA* 1.3 77.2 - - - +
667A MET* 1.3 55.0 + - - +
669A SER* 3.3 10.2 - - - -
670A LEU* 2.9 59.1 + - + +
700A LEU* 4.3 8.7 - - - +
704A LEU* 3.7 31.0 - - + -
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Residues in contact with MET 667 (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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663A LYS* 3.1 37.4 + - + +
664A GLU* 3.4 17.9 - - + +
665A ALA 3.1 0.2 - - - -
666A TYR* 1.3 75.1 - - - +
668A ARG* 1.3 64.7 + - + +
670A LEU* 3.4 5.8 + - - +
671A ASN* 3.1 35.7 + - - +
701A LYS* 5.0 11.5 - - + +
704A LEU* 3.9 22.0 - - + +
705A ASP* 4.9 13.2 - - - +
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Residues in contact with ARG 668 (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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309A ASP* 3.1 54.8 + - - +
310A ILE* 3.6 18.4 - - - +
311A ARG* 3.1 28.2 - - - +
357A ASN* 5.7 3.0 - - - +
378A ASP* 6.3 2.0 - - - +
379A LEU 4.7 4.0 + - - -
664A GLU* 3.0 43.6 + - - +
665A ALA* 3.1 26.5 + - - +
667A MET* 1.3 79.0 - - + +
669A SER* 1.3 52.4 + - - +
671A ASN* 3.3 10.3 + - - +
672A ASN* 2.7 42.5 + - - +
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Residues in contact with SER 669 (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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594A TYR* 5.0 5.5 + - - -
665A ALA 2.8 17.7 + - - -
666A TYR* 3.3 18.2 - - - -
667A MET 3.1 0.2 - - - -
668A ARG* 1.3 74.3 - - - +
670A LEU* 1.3 66.7 + - - +
672A ASN* 3.1 17.0 + - - +
673A PHE* 3.4 7.8 + - - +
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Residues in contact with LEU 670 (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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666A TYR* 2.9 58.0 + - + +
667A MET* 3.8 4.3 - - - +
669A SER* 1.3 75.1 - - - +
671A ASN* 1.3 62.8 + - - +
673A PHE* 3.1 21.4 + - - +
697A LYS* 3.4 40.6 - - + +
700A LEU* 3.9 17.7 - - + +
701A LYS* 3.7 41.3 - - + +
704A LEU* 4.3 8.5 - - + -
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Residues in contact with ASN 671 (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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309A ASP* 5.5 5.9 + - + -
667A MET* 3.1 26.7 + - - +
668A ARG* 3.4 11.1 - - - +
670A LEU* 1.3 76.2 - - - +
672A ASN* 1.3 62.4 + - - +
673A PHE 2.9 5.9 + - - -
674A ARG* 2.9 32.1 + - - +
701A LYS* 3.0 38.4 + - - +
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Residues in contact with ASN 672 (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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308A LYS* 3.5 35.2 - - + +
309A ASP* 2.7 55.3 + - - +
310A ILE* 4.0 5.9 - - - +
668A ARG* 2.7 25.6 + - - +
669A SER* 3.1 9.4 + - - +
671A ASN* 1.3 73.2 - - - +
673A PHE* 1.3 65.9 + - - +
674A ARG* 3.1 10.0 - - - +
675A ALA* 3.1 19.0 + - - +
676A GLU* 4.0 2.3 + - - +
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Residues in contact with PHE 673 (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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669A SER 3.4 5.3 + - - +
670A LEU* 3.1 16.2 + - - +
671A ASN 2.9 0.6 + - - -
672A ASN* 1.3 77.7 - - - +
674A ARG* 1.3 55.1 + - - +
675A ALA 2.7 12.1 + - - -
676A GLU* 2.7 40.8 + - + +
680A GLN* 5.0 4.3 - - + -
681A HIS* 3.2 41.0 + + - -
684A TYR* 3.6 48.7 - + + -
685A TYR* 5.3 4.5 - + - -
697A LYS* 3.6 41.1 - - + +
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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
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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