Contacts of the helix formed by residues 724 - 737 (chain D) in PDB entry 1HWL
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 724 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717D VAL* 3.7 6.5 - - - -
718D ARG* 5.2 10.3 - - + +
723D THR* 1.3 88.6 + - - +
725D THR* 1.3 64.7 + - - +
726D GLU* 3.8 7.9 + - - +
727D ALA* 3.2 24.4 + - - +
728D MET* 3.1 25.6 + - - +
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Residues in contact with THR 725 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714D ALA* 4.7 0.3 - - - -
717D VAL* 3.8 14.4 - - - +
724D THR* 1.3 73.0 - - - +
726D GLU* 1.3 63.7 + - - +
728D MET* 3.3 7.4 + - - +
729D ILE* 3.0 46.7 + - + +
783D ALA* 4.3 6.1 - - + -
788D ASN 5.0 0.9 - - - +
789D GLU* 2.7 29.8 + - - +
790D ASP 3.7 21.3 - - - +
791D LEU* 3.4 24.0 + - + +
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Residues in contact with GLU 726 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724D THR* 3.2 8.2 + - - +
725D THR* 1.3 81.2 - - - +
727D ALA* 1.3 61.4 + - - +
729D ILE* 3.5 9.0 + - - +
730D GLU* 3.1 30.6 + - + +
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Residues in contact with ALA 727 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681C LEU* 5.4 0.2 - - - +
723D THR* 3.5 16.8 - - - +
724D THR* 3.2 20.5 + - - +
726D GLU* 1.3 74.5 - - - +
728D MET* 1.3 65.2 + - - +
730D GLU* 3.3 6.8 + - - +
731D VAL* 3.0 27.9 + - + +
858D ALA* 4.2 14.6 - - + +
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Residues in contact with MET 728 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717D VAL* 4.5 2.0 - - + -
721D LEU* 4.5 2.9 - - + -
723D THR* 3.8 13.5 - - + -
724D THR 3.1 17.5 + - - +
725D THR* 3.4 7.6 - - - +
727D ALA* 1.3 74.5 - - - +
729D ILE* 1.3 59.8 + - - +
731D VAL* 3.2 3.1 + - - +
732D ASN* 2.9 31.7 + - - +
781D MET* 3.9 24.6 - - + +
791D LEU* 3.6 31.0 - - + -
851D LEU* 3.5 33.2 - - + +
854D MET* 3.9 6.8 - - - +
855D ALA* 3.4 33.7 - - + +
858D ALA* 4.3 5.1 - - - +
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Residues in contact with ILE 729 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725D THR* 3.0 32.9 + - + +
726D GLU* 3.8 7.4 - - - +
728D MET* 1.3 75.9 - - - +
730D GLU* 1.3 69.1 + - - +
732D ASN* 3.3 6.2 + - - +
733D ILE* 3.0 41.0 + - + +
781D MET* 4.2 19.5 - - - +
782D GLU* 3.6 2.9 - - - -
783D ALA* 3.3 36.8 - - + +
791D LEU* 4.1 13.2 - - + -
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Residues in contact with GLU 730 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782B GLU* 3.1 17.8 - - - +
595C ARG* 2.8 48.6 + - - +
681C LEU* 3.9 9.9 - - + +
726D GLU* 3.1 23.6 + - + +
727D ALA* 3.6 8.3 - - - +
729D ILE* 1.3 84.8 - - - +
731D VAL* 1.3 62.8 + - - +
733D ILE* 4.9 6.8 - - - +
734D ASN* 2.8 36.7 + - - +
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Residues in contact with VAL 731 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681C LEU* 3.6 37.0 - - + +
682C ALA* 4.4 12.6 - - + -
727D ALA* 3.0 20.8 + - + +
728D MET 3.7 4.0 - - - +
730D GLU* 1.3 75.4 - - - +
732D ASN* 1.3 57.8 + - - +
734D ASN 3.4 0.3 + - - -
735D LYS* 2.9 47.0 + - + +
854D MET* 3.3 25.1 - - + +
857D LEU* 4.4 10.1 - - + -
858D ALA* 3.8 21.3 - - + -
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Residues in contact with ASN 732 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728D MET 2.9 16.5 + - - +
729D ILE 3.7 3.8 - - - +
731D VAL* 1.3 77.6 - - - +
733D ILE* 1.3 64.6 + - - +
736D ASN* 2.8 52.8 + - - +
737D LEU* 3.4 7.3 + - - +
779D THR* 3.0 33.3 + - - +
780D LEU* 3.6 4.0 - - - +
781D MET* 3.4 40.9 + - + +
854D MET* 3.3 12.3 - - + +
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Residues in contact with ILE 733 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733B ILE* 3.8 28.9 - - + -
737B LEU* 4.3 21.1 - - + -
780B LEU* 6.2 0.2 - - + -
729D ILE* 3.0 34.4 + - + +
730D GLU* 4.2 9.6 - - - +
732D ASN* 1.3 77.7 - - + +
734D ASN* 1.3 72.9 + - - +
737D LEU* 3.1 24.3 + - + +
738D VAL* 2.8 28.8 + - + +
781D MET 5.4 4.3 - - - +
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Residues in contact with ASN 734 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780B LEU* 5.2 2.6 - - - +
593C VAL* 4.4 5.4 - - + +
595C ARG* 3.7 22.0 + - - +
642C ASN* 2.7 30.8 + - - +
644C TYR* 2.7 28.4 + - - -
681C LEU* 3.6 20.8 - - + +
730D GLU* 2.8 32.8 + - - +
731D VAL 4.4 0.2 - - - +
733D ILE* 1.3 86.7 - - - +
735D LYS* 1.3 57.3 + - - +
738D VAL* 4.1 12.3 - - - +
739D GLY 3.1 7.9 + - - -
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Residues in contact with LYS 735 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C FBI 2.7 29.0 + - - -
593C VAL* 5.2 3.6 - - + -
682C ALA* 5.2 0.4 - - + -
684C SER* 2.9 37.0 + - - +
685C GLY* 3.9 10.1 - - - -
686C ASN* 2.8 33.9 + - - +
731D VAL* 2.9 21.7 + - + +
734D ASN* 1.3 77.6 - - - +
736D ASN* 1.3 71.0 + - - +
737D LEU 3.3 1.1 - - - -
739D GLY* 3.3 4.0 + - - -
740D SER 3.2 21.7 + - - -
751D ALA* 3.6 21.1 - - - -
854D MET* 3.9 15.0 - - + -
857D LEU* 3.5 16.7 - - + +
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Residues in contact with ASN 736 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686C ASN* 3.3 9.6 + - - +
732D ASN* 2.8 38.0 + - - +
735D LYS* 1.3 88.0 - - - +
737D LEU* 1.3 59.8 + - + +
740D SER* 3.4 2.8 + - - -
749D TYR* 3.2 42.4 - - - +
750D ASN* 3.1 27.4 - - - +
751D ALA* 3.4 12.2 + - - +
779D THR* 3.9 11.9 - - - +
850D GLU* 3.9 1.4 + - - -
854D MET* 3.6 20.3 - - - +
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Residues in contact with LEU 737 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733B ILE* 4.3 16.6 - - + -
737B LEU* 4.3 25.4 - - + +
738B VAL* 4.1 23.3 - - + +
741B ALA* 5.8 0.7 - - + -
732D ASN* 3.4 9.8 + - - +
733D ILE* 3.1 26.4 + - + +
736D ASN* 1.3 85.3 - - - +
738D VAL* 1.3 62.4 + - - +
740D SER* 3.6 1.7 + - - -
741D ALA* 3.0 29.6 + - - +
749D TYR* 4.1 10.1 - - + -
778D ILE* 4.1 19.1 - - + -
779D THR 4.6 3.6 - - - +
780D LEU* 4.0 24.7 - - + -
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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