Contacts of the helix formed by residues 520 - 531 (chain A) 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 520 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507A THR* 4.3 0.2 - - - +
516A ARG* 3.1 45.8 - - - +
518A ILE* 3.8 10.3 - - + +
519A ILE* 1.3 77.2 - - - +
521A PRO* 1.3 78.4 - - + +
522A LYS* 3.3 26.5 - - + +
523A ASP* 2.7 26.0 + - - +
524A ILE* 3.4 3.5 + - - +
47B SER* 4.1 12.8 - - - -
50B ILE* 3.2 14.4 - - - +
70I G 4.9 7.6 - - - +
71I G 3.9 11.7 - - - +
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Residues in contact with PRO 521 (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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520A MET* 1.3 91.9 - - + +
522A LYS* 1.3 50.8 + - + +
524A ILE* 2.9 6.3 + - + +
525A GLN* 2.7 52.8 + - - +
47B SER* 4.6 3.6 - - - +
49B LEU* 3.9 42.2 - - + +
50B ILE* 4.0 8.3 - - + -
53B GLU* 3.8 21.2 - - + +
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Residues in contact with LYS 522 (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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516A ARG* 3.5 29.2 - - - +
520A MET* 3.5 30.2 - - + +
521A PRO* 1.3 79.4 - - + +
523A ASP* 1.3 57.9 + - - +
525A GLN* 3.4 19.9 - - - +
526A LEU* 2.9 29.1 + - - +
713E HIS* 3.8 16.2 + - + +
715E LYS* 5.0 12.7 - - - +
71I G 4.0 11.1 + - - -
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Residues in contact with ASP 523 (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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507A THR* 3.2 27.6 + - + +
510A CYS* 3.9 7.2 - - + +
511A ALA* 3.4 15.6 + - - +
516A ARG* 2.6 40.2 + - - -
519A ILE* 3.5 3.5 - - - -
520A MET* 2.7 26.8 + - - +
521A PRO 3.0 0.2 - - - -
522A LYS* 1.3 75.9 - - - +
524A ILE* 1.3 64.2 + - - +
526A LEU* 3.5 2.1 + - - +
527A ALA* 3.1 23.2 + - - +
713E HIS* 2.8 23.4 + - - -
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Residues in contact with ILE 524 (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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503A LEU* 4.1 17.7 - - + -
504A PHE* 4.6 9.6 - - + -
507A THR* 3.5 25.8 - - + +
520A MET 3.4 2.4 + - - +
521A PRO 2.9 6.5 + - - +
523A ASP* 1.3 75.0 - - - +
525A GLN* 1.3 67.8 + - - +
527A ALA* 3.1 3.3 + - - +
528A ARG* 2.9 42.2 + - - +
534A ARG* 5.9 0.4 - - - +
50B ILE* 3.5 28.5 - - + -
53B GLU* 3.9 23.3 - - + +
54B THR* 4.4 15.7 - - - +
57B VAL* 4.2 11.0 - - + -
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Residues in contact with GLN 525 (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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521A PRO* 2.7 37.8 + - - +
522A LYS* 3.4 17.3 - - - +
524A ILE* 1.3 77.5 - - + +
526A LEU* 1.3 60.5 + - - +
528A ARG* 3.5 1.0 + - - +
529A ARG* 3.1 23.4 + - - +
534A ARG* 3.4 42.5 + - - +
53B GLU* 3.8 13.9 + - - +
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Residues in contact with LEU 526 (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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510A CYS* 3.7 17.0 - - - -
522A LYS 2.9 17.8 + - - +
523A ASP 3.9 4.7 - - - +
525A GLN* 1.3 73.0 - - - +
527A ALA* 1.3 66.5 + - - +
529A ARG* 3.3 5.6 + - + +
530A ILE* 3.1 34.6 + - + +
709E LEU* 4.0 38.1 - - + +
710E CYS* 4.3 14.1 - - - -
713E HIS* 3.2 43.5 - - + +
726E LEU* 5.0 1.3 - - + -
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Residues in contact with ALA 527 (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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503A LEU* 4.1 12.1 - - + -
506A ASP* 3.9 28.0 - - + -
507A THR* 4.3 4.5 - - - +
510A CYS* 4.2 10.1 - - - -
523A ASP 3.1 14.5 + - - +
524A ILE 3.1 4.8 + - - +
526A LEU* 1.3 76.2 - - - +
528A ARG* 1.3 66.3 + - - +
530A ILE 3.3 1.6 + - - -
531A ARG* 3.0 29.9 + - - +
730E ILE* 3.7 9.9 - - + +
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Residues in contact with ARG 528 (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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499A TYR* 3.8 4.1 + - - -
503A LEU* 3.9 20.2 - - + -
524A ILE* 2.9 26.1 + - - +
525A GLN 4.0 3.1 - - - +
527A ALA* 1.3 77.1 - - - +
529A ARG* 1.3 60.1 + - - +
531A ARG* 3.3 7.3 + - - +
532A GLY 3.3 2.9 + - - -
533A GLU* 3.0 75.2 + - + +
534A ARG* 2.8 36.7 + - + +
57B VAL* 4.0 33.6 - - - +
60B VAL* 5.0 19.7 - - - +
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Residues in contact with ARG 529 (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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525A GLN 3.1 17.7 + - - +
526A LEU* 3.7 8.7 - - + +
527A ALA 3.1 0.6 - - - -
528A ARG* 1.3 75.2 - - - +
530A ILE* 1.3 65.0 + - - +
532A GLY* 3.1 13.5 + - - -
534A ARG* 3.8 23.7 - - + +
535A ALA* 3.2 42.1 + - + +
705E GLU* 5.0 14.1 + - - +
706E ASP* 3.7 18.8 + - - +
709E LEU* 3.2 34.2 - - + +
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Residues in contact with ILE 530 (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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526A LEU* 3.1 27.8 + - + +
529A ARG* 1.3 78.7 - - + +
531A ARG* 1.3 59.7 + - - +
532A GLY* 3.1 1.5 + - - -
706E ASP* 4.0 31.4 - - + +
709E LEU* 5.4 2.2 - - + -
710E CYS* 3.3 34.5 - - - -
727E ALA* 3.6 28.9 - - + +
730E ILE* 4.0 28.5 - - + -
731E ARG* 3.6 23.8 + - + +
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Residues in contact with ARG 531 (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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499A TYR* 3.3 25.7 + - - -
502A ALA* 3.8 12.5 + - - +
503A LEU* 3.8 39.9 - - - +
506A ASP* 3.1 27.1 + - - -
527A ALA 3.0 23.7 + - - +
528A ARG* 3.5 7.6 - - - +
529A ARG 3.0 0.4 - - - -
530A ILE* 1.3 78.2 - - - +
532A GLY* 1.3 59.4 + - - +
533A GLU* 2.9 35.0 + - - +
95B ARG* 4.7 8.7 - - - +
899C ARG* 4.6 10.9 + - - -
730E ILE* 3.9 20.1 + - + +
731E ARG* 5.5 1.8 - - - +
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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