Contacts of the helix formed by residues 515 - 524 (chain A) in PDB entry 1P0P
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 ARG 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A LYS* 3.3 18.8 + - - +
391A ASP* 4.6 12.4 + - - -
395A ASP* 3.0 24.3 + - - +
399A ILE* 3.5 32.4 - - + +
400A CYS* 4.9 0.2 - - - -
420A TYR* 2.8 29.7 + - - -
513A LYS 3.3 1.6 + - - -
514A LEU* 1.3 90.9 - - + +
516A ALA* 1.3 65.3 + - - +
517A GLN 3.4 2.7 - - - -
518A GLN* 3.2 35.6 + - + +
519A CYS* 2.9 35.4 + - - +
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Residues in contact with ALA 516 (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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513A LYS* 3.2 27.0 + - + +
514A LEU 3.1 4.6 + - - -
515A ARG* 1.3 75.4 - - - +
517A GLN* 1.3 64.5 + - + +
518A GLN* 4.0 0.2 + - - -
519A CYS* 4.2 3.0 - - - +
520A ARG* 3.1 53.3 + - - +
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Residues in contact with GLN 517 (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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372A HIS* 3.5 21.1 - - + +
515A ARG 3.4 0.8 - - - -
516A ALA* 1.3 80.5 - - + +
518A GLN* 1.3 70.5 + - - +
520A ARG* 3.4 23.0 + - - +
521A PHE 3.3 14.9 + - - -
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Residues in contact with GLN 518 (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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372A HIS* 3.6 13.9 - - + +
373A TYR* 3.5 27.5 - - + +
395A ASP* 3.5 21.0 + - + +
400A CYS* 4.0 0.4 - - - -
515A ARG* 3.4 40.6 - - + +
517A GLN* 1.3 82.5 + - - +
519A CYS* 1.3 62.2 + - - +
521A PHE* 3.3 4.0 + - - +
522A TRP* 3.0 29.8 + - - -
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Residues in contact with CYS 519 (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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400A CYS* 2.0 59.0 - - + +
403A LEU* 3.9 22.7 - - + -
404A GLU* 5.9 0.9 - - - +
514A LEU 5.1 0.4 - - - +
515A ARG* 2.9 25.0 + - - +
516A ALA* 4.4 2.5 - - - +
518A GLN* 1.3 73.1 - - - +
520A ARG* 1.3 58.2 + - - +
521A PHE 3.0 2.2 - - - -
522A TRP 4.3 0.4 - - - +
523A THR* 2.6 43.6 + - - +
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Residues in contact with ARG 520 (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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513A LYS* 5.3 7.1 - - - +
516A ALA* 3.1 51.5 + - - +
517A GLN* 3.5 24.0 - - - +
519A CYS* 1.3 77.3 - - - +
521A PHE* 1.3 58.1 + - - +
523A THR* 5.0 0.7 - - - -
524A SER* 3.1 40.2 + - - +
525A PHE* 3.6 1.7 + - - +
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Residues in contact with PHE 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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368A SER* 3.8 33.4 - - - -
369A ILE* 3.8 13.0 - - + -
372A HIS* 3.6 39.5 - + + +
373A TYR* 4.6 2.2 - + - -
517A GLN 3.3 1.8 + - - -
518A GLN 3.3 8.0 + - - +
519A CYS 3.0 0.6 - - - -
520A ARG* 1.3 79.7 - - - +
522A TRP* 1.3 108.2 + + - +
525A PHE* 3.1 46.9 + + + +
526A PHE* 3.0 32.4 + + + -
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Residues in contact with TRP 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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358A PHE* 3.6 22.0 - + - -
369A ILE* 3.7 14.6 - - + -
373A TYR* 2.7 36.0 + + - -
392A VAL* 3.9 12.6 - - + -
395A ASP* 3.6 16.7 - - + +
396A TYR* 3.2 48.1 - + + +
400A CYS* 3.9 18.4 - - + -
518A GLN 3.0 23.8 + - - +
519A CYS 4.1 1.8 - - - +
521A PHE* 1.3 94.9 - + - +
523A THR* 1.3 59.0 + - - +
526A PHE* 3.5 36.7 - + - +
527A PRO* 3.0 23.9 - - - +
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Residues in contact with THR 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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400A CYS* 4.4 9.5 + - - +
404A GLU* 3.0 45.8 + - + +
408A LYS* 6.2 0.2 - - - -
519A CYS* 2.6 31.6 + - - +
520A ARG* 5.0 0.4 - - - -
522A TRP* 1.3 76.3 - - - +
524A SER* 1.3 62.3 + - - +
527A PRO* 3.6 13.9 - - - +
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Residues in contact with SER 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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520A ARG* 3.1 25.6 + - - +
523A THR* 1.3 84.6 - - - +
525A PHE* 1.3 64.7 + - - +
527A PRO* 3.8 5.5 - - - +
528A LYS* 3.2 27.2 - - - +
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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