Contacts of the helix formed by residues 750 - 765 (chain D) in PDB entry 1P93
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 PRO 750 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564D ASN* 3.0 37.7 - - + +
565D MET* 3.1 27.1 - - + +
568D GLY* 3.8 11.2 - - - -
749D PHE* 1.3 90.5 - - + +
751D GLU* 1.3 66.2 + - - +
752D MET* 3.1 4.7 + - + +
753D LEU* 3.1 28.7 + - + +
754D ALA* 3.2 9.4 + - - +
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Residues in contact with GLU 751 (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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634A MET 5.2 0.2 - - - +
635A THR 3.9 11.7 + - - +
636A LEU 2.6 28.3 - - - +
637A PRO* 3.7 10.1 - - + -
638A ASP* 2.7 38.5 + - - +
639A MET 3.8 1.7 + - - -
640A TYR* 5.0 2.4 + - - +
641A ASP* 3.9 8.9 + - - +
749D PHE 3.8 1.0 + - - -
750D PRO* 1.3 70.5 - - - +
752D MET* 1.3 67.9 + - - +
754D ALA* 2.9 25.3 + - + +
755D GLU* 3.2 8.0 + - - +
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Residues in contact with MET 752 (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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635A THR* 5.4 6.4 + - + -
568D GLY* 3.9 20.4 - - - +
571D VAL* 4.3 12.3 - - + -
572D ILE* 3.9 31.0 - - + -
575D VAL* 6.1 1.8 - - - -
750D PRO* 3.1 3.8 - - + +
751D GLU* 1.3 84.4 - - - +
753D LEU* 1.3 59.5 + - + +
754D ALA 3.2 0.3 + - - -
755D GLU* 3.6 10.9 + - + -
756D ILE* 3.0 34.8 - - + +
943H LEU* 3.4 34.1 - - + -
944H LEU* 4.2 15.7 - - + +
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Residues in contact with LEU 753 (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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564D ASN* 3.4 27.1 - - + +
567D GLY 4.5 1.1 - - - -
568D GLY* 3.9 9.4 - - - +
571D VAL* 3.5 32.5 - - + -
600D TRP* 3.9 24.0 - - + -
749D PHE* 4.4 15.0 - - + -
750D PRO* 3.1 22.8 + - + +
752D MET* 1.3 76.2 - - - +
754D ALA* 1.3 59.2 + - - +
756D ILE* 3.6 13.2 - - + -
757D ILE* 2.9 40.7 + - + +
4999D DEX 4.2 17.0 - - + +
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Residues in contact with ALA 754 (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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740D PHE* 4.9 14.8 - - + -
749D PHE* 5.1 4.2 - - + +
750D PRO 3.2 7.3 + - - +
751D GLU* 2.9 21.9 + - + +
753D LEU* 1.3 74.6 - - - +
755D GLU* 1.3 64.4 + - - +
756D ILE 3.0 1.1 - - - -
758D THR* 2.6 37.2 + - - +
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Residues in contact with GLU 755 (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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751D GLU 3.2 6.6 + - - +
752D MET* 4.0 16.6 - - + +
754D ALA* 1.3 76.7 - - - +
756D ILE* 1.3 55.5 + - + +
758D THR* 3.7 4.2 - - - +
759D ASN* 2.8 46.0 + - + +
942H ALA* 3.0 48.9 + - - +
943H LEU* 3.9 6.5 + - + +
944H LEU* 5.1 7.2 - - + +
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Residues in contact with ILE 756 (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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571D VAL* 4.3 13.0 - - + -
596D LEU 5.7 0.2 - - - +
597D GLN* 4.5 11.9 - - + +
600D TRP* 3.4 39.0 - - + +
752D MET* 3.0 35.0 - - + +
753D LEU* 3.6 27.4 - - + +
754D ALA 3.0 0.6 - - - -
755D GLU* 1.3 75.3 - - + +
757D ILE* 1.3 72.3 + - + +
758D THR 2.6 3.1 + - - -
759D ASN* 2.7 7.0 + - - +
760D GLN* 2.7 30.8 + - + -
944H LEU* 6.2 3.6 - - + -
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Residues in contact with ILE 757 (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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600D TRP* 4.7 12.8 - - + +
736D CYS* 3.6 18.8 - - - -
737D PHE* 3.2 33.5 - - + -
740D PHE* 3.3 25.8 - - + -
749D PHE* 3.6 35.9 - - + -
753D LEU* 2.9 29.5 + - + +
754D ALA 4.2 0.7 - - - +
756D ILE* 1.3 79.3 - - - +
758D THR* 1.3 49.8 + - - +
760D GLN* 4.6 0.9 - - - -
761D ILE* 3.4 17.6 + - + -
762D PRO* 2.8 32.2 - - - +
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Residues in contact with THR 758 (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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740D PHE* 3.8 18.0 - - - -
754D ALA* 2.6 24.6 + - - +
755D GLU* 3.7 4.7 - - - +
756D ILE 2.6 4.0 + - - -
757D ILE* 1.3 70.9 - - - +
759D ASN* 1.3 64.7 + - - +
762D PRO* 2.6 40.2 - - + +
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Residues in contact with ASN 759 (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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597D GLN* 3.4 28.7 + - - +
755D GLU* 2.8 31.3 + - + +
756D ILE* 2.7 7.5 + - - +
758D THR* 1.3 76.7 - - - +
760D GLN* 1.3 85.8 + - - +
762D PRO* 4.5 0.3 - - - +
763D LYS* 2.9 43.6 + - - +
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Residues in contact with GLN 760 (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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594D THR 5.6 0.2 + - - -
597D GLN* 3.1 34.8 + - + +
598D TYR* 4.1 18.2 - - - +
600D TRP* 5.2 3.5 + - + +
733D LEU* 5.2 4.0 - - - +
756D ILE* 2.7 26.6 + - + +
757D ILE* 4.2 0.7 - - - +
759D ASN* 1.3 88.1 + - - +
761D ILE* 1.3 64.7 + - + +
762D PRO* 2.6 19.9 - - - -
763D LYS* 2.9 27.9 - - - +
764D TYR* 3.2 40.5 + - - +
769D ILE* 4.2 11.3 - - - +
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Residues in contact with ILE 761 (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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600D TRP* 6.3 0.4 - - - +
733D LEU* 3.9 34.5 - - + +
734D ASN* 5.9 2.0 - - - +
736D CYS* 5.0 0.4 - - - -
737D PHE* 3.0 63.3 - - + +
757D ILE* 3.4 19.3 + - + +
760D GLN* 1.3 82.9 + - + +
762D PRO* 1.4 60.2 - - - +
764D TYR* 2.7 52.4 - - + +
765D SER* 2.8 18.2 + - - +
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Residues in contact with PRO 762 (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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737D PHE* 3.6 19.1 - - + -
740D PHE* 6.2 0.2 - - + -
757D ILE 2.8 19.7 - - - +
758D THR* 2.6 36.8 - - + +
759D ASN 4.5 0.2 - - - +
760D GLN 2.6 5.3 - - - +
761D ILE* 1.4 80.6 - - + +
763D LYS* 1.3 67.0 + - - +
765D SER* 3.1 14.6 + - - +
766D ASN* 3.6 3.6 - - - +
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Residues in contact with LYS 763 (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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594D THR* 5.5 3.2 - - - +
597D GLN* 3.2 18.0 + - - +
759D ASN* 2.9 44.8 + - - +
760D GLN* 2.9 33.8 - - - +
762D PRO* 1.3 76.5 - - - +
764D TYR* 1.3 65.0 + - - +
765D SER 2.6 9.2 + - - -
766D ASN* 2.5 38.8 + - - +
768D ASN* 3.9 10.3 - - - +
769D ILE* 5.0 4.7 - - - -
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Residues in contact with TYR 764 (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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598D TYR* 5.1 12.6 - + - -
730D GLU* 5.0 5.2 + - - +
733D LEU* 4.1 26.8 - - + +
734D ASN* 4.3 11.3 + - - -
760D GLN* 3.2 36.3 + - - +
761D ILE* 2.7 53.1 - - + +
763D LYS* 1.3 79.8 - - + +
765D SER* 1.3 67.6 + - - +
766D ASN 2.9 3.3 + - - -
767D GLY* 3.1 15.1 + - - -
768D ASN* 3.3 14.4 + - - +
769D ILE* 3.5 26.5 + - + +
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Residues in contact with SER 765 (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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737D PHE* 5.7 1.7 - - - -
761D ILE* 2.8 19.2 + - - +
762D PRO* 3.1 13.4 + - - +
763D LYS 2.6 6.7 + - - -
764D TYR* 1.3 83.2 - - - +
766D ASN* 1.3 55.8 + - - -
767D GLY 3.0 9.9 + - - -
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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