Contacts of the helix formed by residues 720 - 732 (chain E) in PDB entry 1P3M
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 MET 720 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716E ARG* 3.1 43.7 - - - +
718E ILE* 3.5 11.2 - - + +
719E ILE* 1.3 80.3 - - - +
721E PRO* 1.3 79.8 - - + +
722E LYS* 3.1 28.0 - - + +
723E ASP* 2.8 25.3 + - - +
724E ILE* 3.3 4.2 + - - +
247F SER* 3.9 11.7 - - - -
250F ILE* 3.3 9.7 - - - +
217J G 5.5 5.2 - - - +
218J A 3.9 16.2 - - - +
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Residues in contact with PRO 721 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720E MET* 1.3 88.2 - - + +
722E LYS* 1.3 50.3 + - - +
724E ILE* 3.0 6.3 + - + +
725E GLN* 2.7 46.2 + - - +
247F SER* 4.4 3.4 - - - +
249F LEU* 3.6 46.4 - - + +
250F ILE* 3.4 8.0 - - + -
253F GLU* 3.5 32.9 - - + +
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Residues in contact with LYS 722 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A HIS* 3.9 29.1 + - + +
515A LYS* 4.5 19.6 - - - +
716E ARG* 4.3 7.4 - - - +
720E MET* 3.5 39.8 - - + +
721E PRO* 1.3 77.9 - - - +
723E ASP* 1.3 59.8 + - - +
725E GLN* 3.4 17.7 + - - +
726E LEU* 2.9 29.1 + - - +
218J A 4.8 4.9 + - - -
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Residues in contact with ASP 723 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A HIS* 2.7 33.1 + - - -
707E THR* 3.5 23.1 - - + +
710E CYS* 4.1 5.7 - - + +
711E ALA* 3.1 21.4 + - - +
716E ARG* 2.7 34.7 + - - -
720E MET* 2.8 26.2 + - - +
722E LYS* 1.3 74.9 - - - +
724E ILE* 1.3 64.0 + - - +
726E LEU* 3.1 3.3 + - - +
727E ALA* 3.0 23.9 + - - +
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Residues in contact with ILE 724 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703E LEU* 4.3 17.3 - - + -
704E PHE* 4.4 9.0 - - + -
707E THR* 3.4 28.9 - - + +
720E MET 3.3 6.9 + - - +
721E PRO* 3.0 9.0 + - + +
723E ASP* 1.3 76.4 - - - +
725E GLN* 1.3 59.3 + - - +
727E ALA* 3.3 3.0 + - - +
728E ARG* 3.0 46.2 + - + +
734E ARG* 4.9 2.2 - - - +
250F ILE* 3.9 21.5 - - + -
253F GLU* 4.2 17.7 - - + -
254F THR* 3.8 24.0 - - + +
257F VAL* 4.3 14.8 - - + -
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Residues in contact with GLN 725 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721E PRO* 2.7 29.5 + - - +
722E LYS* 3.5 15.1 - - - +
724E ILE* 1.3 74.7 - - - +
726E LEU* 1.3 66.1 + - - +
728E ARG* 3.4 2.0 + - - +
729E ARG* 3.0 23.7 + - - +
734E ARG* 2.8 38.4 - - - +
253F GLU* 3.3 28.2 + - - +
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Residues in contact with LEU 726 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A LEU* 4.1 30.7 - - + +
510A CYS* 4.3 15.7 - - - -
513A HIS* 3.3 46.4 - - + +
526A LEU* 5.0 1.3 - - + -
710E CYS* 3.8 13.5 - - - -
722E LYS 2.9 17.5 + - - +
723E ASP 3.1 4.0 + - - +
725E GLN* 1.3 75.7 - - - +
727E ALA* 1.3 64.8 + - - +
729E ARG* 3.2 4.6 + - + +
730E ILE* 3.0 41.0 + - + +
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Residues in contact with ALA 727 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A ILE* 3.6 14.1 - - + +
703E LEU* 4.2 9.9 - - + -
706E ASP* 3.9 28.5 - - + -
707E THR* 4.2 7.9 - - - +
710E CYS* 4.1 6.2 - - - -
723E ASP 3.0 12.6 + - - +
724E ILE* 3.6 9.4 - - - +
725E GLN 3.2 0.2 - - - -
726E LEU* 1.3 78.7 - - - +
728E ARG* 1.3 57.1 + - - +
730E ILE 3.3 0.2 + - - -
731E ARG* 2.9 35.0 + - - +
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Residues in contact with ARG 728 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699E TYR* 3.4 13.9 + - - -
703E LEU* 4.0 22.7 - - + -
724E ILE* 3.0 22.6 + - + +
725E GLN 4.0 0.4 - - - +
727E ALA* 1.3 75.5 - - - +
729E ARG* 1.3 59.9 + - - +
731E ARG* 3.7 7.6 - - - +
732E GLY 3.2 3.6 + - - -
733E GLU* 2.9 66.2 + - + +
734E ARG* 2.9 55.1 + - + +
257F VAL* 3.9 23.3 + - - +
260F VAL* 4.9 21.6 - - - +
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Residues in contact with ARG 729 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A ASP* 4.6 4.5 - - - +
509A LEU* 3.3 42.7 - - + +
725E GLN 3.0 18.4 + - - +
726E LEU* 3.5 9.2 - - + +
727E ALA 3.1 0.2 - - - -
728E ARG* 1.3 75.6 - - - +
730E ILE* 1.3 67.6 + - + +
732E GLY* 3.2 8.8 + - - -
734E ARG* 3.8 14.9 + - + +
735E ALA* 3.3 51.7 + - + +
1110G ASN* 5.7 3.2 - - - +
1112G GLN* 4.6 12.5 + - - +
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Residues in contact with ILE 730 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A ASP* 4.0 33.7 - - + +
509A LEU* 5.4 0.7 - - + -
510A CYS* 3.5 32.1 - - - -
527A ALA* 3.7 27.1 - - - +
530A ILE* 4.0 24.0 - - + -
531A ARG* 3.9 19.3 + - + +
726E LEU* 3.0 34.5 + - + +
727E ALA 3.9 2.7 - - - +
729E ARG* 1.3 78.6 - - + +
731E ARG* 1.3 62.8 + - - +
732E GLY* 3.2 1.4 + - - -
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Residues in contact with ARG 731 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A ILE* 3.6 22.7 - - + +
531A ARG* 5.5 1.8 - - - +
699E TYR* 3.5 23.2 + - - -
702E ALA* 3.4 12.5 + - - +
703E LEU* 3.2 48.7 - - - +
706E ASP* 2.8 27.4 + - - -
727E ALA 2.9 25.1 + - - +
728E ARG* 3.7 5.6 - - - +
730E ILE* 1.3 76.8 - - - +
732E GLY* 1.3 61.1 + - - +
733E GLU* 2.9 32.1 + - - +
295F ARG* 5.1 6.2 - - - +
1099G ARG* 5.1 8.5 + - - -
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Residues in contact with GLY 732 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728E ARG 3.2 2.8 + - - -
729E ARG 3.2 7.8 + - - -
730E ILE 3.1 5.3 - - - -
731E ARG* 1.3 82.3 - - - +
733E GLU* 1.3 64.0 + - - +
734E ARG 3.6 0.7 - - - -
735E ALA* 4.5 11.2 - - - -
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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