Contacts of the helix formed by residues 637 - 651 (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 LYS 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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529A GLU 2.8 28.9 + - - +
530A PHE* 3.6 40.5 - - + +
531A ILE 3.5 14.3 + - - -
532A PRO* 4.4 1.6 - - + -
533A THR* 4.6 7.6 - - - +
616A LEU* 3.8 10.2 - - + +
634A TYR* 4.2 2.2 + - - +
635A ASN 3.5 0.2 - - - -
636A ASP* 1.3 111.4 - - + +
638A GLN* 1.3 67.1 + - - +
639A PRO* 3.5 2.7 - - - -
640A ILE* 3.0 31.5 + - + +
641A LEU 3.5 2.9 + - - -
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Residues in contact with GLN 638 (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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572A ALA* 2.8 46.4 + - - +
574A LEU* 3.8 21.7 - - + +
616A LEU* 3.6 20.2 - - + +
631A VAL* 3.4 24.9 + - + +
632A LYS 3.7 2.8 - - - -
633A GLY 3.6 14.1 + - - +
634A TYR 3.9 2.3 + - - +
635A ASN* 2.9 29.5 + - - +
637A LYS* 1.3 76.0 - - - +
639A PRO* 1.4 66.2 - - + +
641A LEU* 3.1 14.6 + - - +
642A LEU* 3.2 13.0 + - - +
733A ILE* 5.4 1.7 - - - +
741A ILE* 5.8 1.2 - - - +
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Residues in contact with PRO 639 (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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574A LEU* 5.6 0.6 - - + -
635A ASN 3.6 7.6 - - - +
636A ASP 4.5 4.5 - - - +
637A LYS* 3.7 2.2 - - - -
638A GLN* 1.4 92.5 - - + +
640A ILE* 1.3 70.3 + - + +
642A LEU* 3.7 10.3 - - + +
643A LYS* 3.0 24.8 + - - +
741A ILE* 4.5 24.7 - - + -
744A MET* 4.3 18.2 - - + +
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Residues in contact with ILE 640 (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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530A PHE* 4.1 11.0 - - + -
607A TYR* 3.5 21.1 - - - +
636A ASP 5.6 0.2 - - - +
637A LYS* 3.0 28.4 + - + +
639A PRO* 1.3 84.7 - - + +
641A LEU* 1.3 63.3 + - - +
643A LYS* 3.2 5.5 + - - +
644A LYS* 3.0 20.4 + - + +
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Residues in contact with LEU 641 (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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530A PHE* 4.4 5.1 - - + -
604A LEU* 6.0 1.3 - - + -
607A TYR* 4.0 22.0 - - + -
608A ALA* 4.4 13.2 - - + -
611A ALA* 4.2 18.8 - - + -
616A LEU* 3.9 33.2 - - + +
617A SER 4.5 2.0 - - - -
618A TYR* 4.3 26.9 - - + -
631A VAL* 4.4 11.4 - - + -
637A LYS 3.5 1.2 + - - -
638A GLN 3.1 8.5 + - - +
640A ILE* 1.3 77.9 - - - +
642A LEU* 1.3 54.8 + - - +
644A LYS* 2.9 8.2 + - + +
645A ILE* 2.8 52.3 + - + +
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Residues in contact with LEU 642 (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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574A LEU* 3.9 15.9 - - + -
576A PHE* 3.9 12.6 - - + -
629A LEU* 4.1 15.5 - - + -
631A VAL* 4.3 16.0 - - + +
638A GLN 3.2 9.8 + - - +
639A PRO* 3.7 11.4 - - + +
641A LEU* 1.3 77.1 - - - +
643A LYS* 1.3 57.5 - - - +
645A ILE* 2.9 11.1 + - - +
646A ILE* 2.9 52.7 + - + +
741A ILE* 3.8 31.6 - - + +
744A MET* 5.4 6.1 - - - -
745A VAL* 3.9 11.7 - - + -
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Residues in contact with LYS 643 (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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639A PRO 3.0 15.8 + - - +
640A ILE* 3.6 5.6 - - - +
642A LEU* 1.3 78.9 - - - +
644A LYS* 1.3 66.9 + - - +
646A ILE* 3.9 4.8 - - - +
647A GLU* 2.9 65.9 + - + +
744A MET* 3.5 38.1 - - + -
748A THR* 4.5 11.2 - - - +
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Residues in contact with LYS 644 (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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604A LEU* 4.4 11.3 - - + +
607A TYR* 3.6 57.5 - - + +
640A ILE* 3.0 11.5 + - + +
641A LEU* 2.9 8.5 + - + +
643A LYS* 1.3 80.5 - - - +
645A ILE* 1.3 58.0 + - - +
647A GLU* 3.8 14.1 - - + +
648A LYS* 2.9 51.3 + - + +
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Residues in contact with ILE 645 (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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600A LEU* 4.4 8.2 - - + +
604A LEU* 4.2 26.2 - - + -
618A TYR* 3.6 38.4 - - + -
620A LEU* 4.5 8.7 - - + -
629A LEU* 4.5 13.7 - - + -
631A VAL* 4.3 8.7 - - + -
641A LEU* 2.8 39.3 + - + +
642A LEU* 3.4 10.8 - - - +
644A LYS* 1.3 76.9 - - - +
646A ILE* 1.3 63.4 + - - +
648A LYS* 3.1 4.3 + - - +
649A MET* 2.9 35.5 + - + +
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Residues in contact with ILE 646 (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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576A PHE* 6.1 0.4 - - + -
578A PHE* 4.3 7.9 - - + -
629A LEU* 4.3 10.3 - - + -
642A LEU* 2.9 42.5 + - + +
643A LYS* 4.0 3.8 - - - +
645A ILE* 1.3 70.1 - - - +
647A GLU* 1.3 63.8 + - - +
649A MET* 2.8 41.4 + - + +
650A ALA* 3.0 12.6 + - - +
744A MET* 6.3 0.9 - - - -
745A VAL* 3.8 37.0 - - + +
748A THR* 3.7 27.6 - - + -
749A LEU* 4.0 19.7 - - + -
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Residues in contact with GLU 647 (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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643A LYS* 2.9 50.5 + - - +
644A LYS* 3.8 15.0 - - + +
646A ILE* 1.3 77.5 - - - +
648A LYS* 1.3 61.8 + - + +
650A ALA* 3.3 2.0 + - - +
651A THR* 3.0 33.0 + - + +
748A THR* 3.5 16.8 - - + +
752A HIS* 4.5 18.6 + - + +
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Residues in contact with LYS 648 (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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600A LEU* 3.9 11.0 - - + -
603A SER* 3.4 28.1 + - - +
604A LEU* 4.0 24.2 - - + -
644A LYS* 2.9 43.2 + - + +
645A ILE 3.1 4.2 + - - +
647A GLU* 1.3 73.4 - - + +
649A MET* 1.3 65.5 + - - +
651A THR* 3.6 4.2 - - - +
652A PHE* 3.1 37.9 + - + +
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Residues in contact with MET 649 (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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578A PHE* 5.1 9.6 - - + -
596A TYR* 2.8 32.3 + - + +
597A LEU* 5.3 1.1 - - + -
600A LEU* 3.6 25.8 - - + +
620A LEU* 4.9 11.0 - - + -
627A MET* 4.9 16.8 - - - +
629A LEU* 5.0 4.0 - - + -
645A ILE* 2.9 20.8 + - + +
646A ILE* 2.8 63.1 + - + +
648A LYS* 1.3 73.3 - - - +
650A ALA* 1.3 63.1 + - + +
651A THR 3.5 0.2 + - - -
652A PHE* 3.6 9.2 + - - +
716A ILE* 4.3 1.2 - - - +
720A LEU* 3.5 15.4 - - + +
749A LEU* 5.3 5.8 - - + -
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Residues in contact with ALA 650 (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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646A ILE 3.0 14.1 + - - +
647A GLU* 3.3 3.6 + - - +
649A MET* 1.3 78.6 - - - +
651A THR* 1.3 59.8 + - - +
652A PHE 3.5 0.8 + - - -
716A ILE* 6.0 0.4 - - - -
720A LEU* 4.1 13.0 - - - +
748A THR 4.2 8.7 - - - +
749A LEU* 4.3 16.2 - - + -
752A HIS* 3.3 43.2 - - + +
753A ALA* 4.4 6.0 - - + +
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Residues in contact with THR 651 (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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647A GLU* 3.0 24.8 + - + +
648A LYS* 3.6 4.4 + - - +
650A ALA* 1.3 83.1 - - - +
652A PHE* 1.3 63.7 + - - +
653A GLU* 3.5 9.2 + - - +
752A HIS* 3.4 41.3 - - + +
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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