Contacts of the helix formed by residues 523 - 531 (chain A) in PDB entry 1PS9
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 ASN 523 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A PRO* 4.2 1.7 - - - +
519A SER 4.3 10.1 - - - +
520A THR* 3.3 12.8 + - + +
521A SER 3.7 0.2 - - - -
522A GLN* 1.3 80.4 + - - +
524A ILE* 1.3 53.0 + - - +
525A ALA* 3.4 9.5 + - - +
526A GLY* 2.8 30.7 + - - +
527A PHE* 2.7 32.7 + - - +
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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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264A PRO* 4.0 14.3 - - + +
265A ARG 3.8 13.7 - - - +
266A GLY 3.6 21.5 - - - +
267A ALA* 3.5 30.5 - - + +
270A TRP* 3.9 17.5 - - + +
301A ARG* 6.4 0.2 - - - +
522A GLN 5.8 0.2 - - - -
523A ASN* 1.3 72.5 + - - +
525A ALA* 1.3 59.5 + - - +
527A PHE* 3.3 1.7 + - - +
528A CYS* 3.0 31.5 + - - -
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Residues in contact with ALA 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ASN* 3.4 7.2 + - - +
524A ILE* 1.3 78.7 - - - +
526A GLY* 1.3 57.9 + - - +
528A CYS* 3.3 6.9 + - - +
529A ASN* 2.9 28.8 + - - +
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Residues in contact with GLY 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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520A THR* 3.7 11.0 - - - -
523A ASN* 2.8 24.1 + - - -
525A ALA* 1.3 74.7 - - - +
527A PHE* 1.3 58.2 + - - +
529A ASN* 3.1 7.3 + - - +
530A GLU* 2.8 34.3 + - - +
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Residues in contact with PHE 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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256A ILE* 4.6 0.4 - - + -
257A PRO* 3.4 28.9 - - + -
262A PRO* 4.0 10.1 - - + -
263A VAL* 4.1 17.9 - - + -
264A PRO* 3.5 28.5 - - + -
267A ALA* 4.9 3.6 - - + -
268A PHE* 4.1 12.1 - + - -
520A THR* 3.4 26.3 - - - +
523A ASN 2.7 19.9 + - - +
524A ILE 3.5 4.0 - - - +
526A GLY* 1.3 71.9 - - - +
528A CYS* 1.3 73.6 + - - +
530A GLU 3.4 0.2 + - - -
531A TRP* 3.1 58.1 + + - +
533A ILE* 4.1 19.7 - - + -
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Residues in contact with CYS 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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267A ALA 4.8 1.8 - - - -
268A PHE* 5.2 1.3 - - - -
270A TRP* 3.9 37.5 - - + -
524A ILE* 3.0 24.1 + - - +
525A ALA* 3.6 7.6 - - - +
527A PHE* 1.3 83.6 - - - +
529A ASN* 1.3 61.7 + - - +
531A TRP 4.0 0.2 - - - -
532A GLY 3.2 2.6 + - - -
533A ILE* 2.9 59.9 + - + +
535A SER* 6.1 3.8 - - - +
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Residues in contact with ASN 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 ALA 2.9 17.7 + - - +
526A GLY* 3.5 8.4 + - - +
528A CYS* 1.3 77.0 - - - +
530A GLU* 1.3 68.0 + - - +
532A GLY* 3.4 9.6 + - - -
533A ILE 5.3 0.9 - - - -
546A GLN* 4.2 16.5 + - - -
549A GLN* 3.7 26.1 + - - +
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Residues in contact with GLU 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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515A GLN* 5.8 1.4 + - - -
516A PRO* 5.7 1.7 - - - +
518A GLU 5.2 2.8 - - - +
520A THR* 3.2 38.5 + - + +
526A GLY 2.8 15.4 + - - +
527A PHE 3.9 3.6 - - - +
529A ASN* 1.3 79.0 - - - +
531A TRP* 1.3 67.6 + - + +
549A GLN 2.9 38.6 + - - +
550A ILE* 3.2 26.0 - - + +
551A PRO* 3.2 28.8 - - + +
582A THR* 6.0 1.6 - - - +
586A ARG* 5.3 8.2 + - - -
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Residues in contact with TRP 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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255A ARG 3.5 23.3 - - - -
256A ILE* 3.4 39.0 - - + +
257A PRO* 3.5 32.5 - - + +
262A PRO* 6.2 2.1 - - + +
520A THR* 4.9 4.6 + - - -
527A PHE* 3.1 56.5 + + - +
530A GLU* 1.3 87.1 + - + +
532A GLY* 1.3 62.5 + - - +
533A ILE* 3.5 6.7 - - + -
548A MET* 3.8 37.5 - - - +
550A ILE* 5.2 8.1 - - + -
577A TRP* 5.2 0.4 - + - -
578A ILE* 4.2 13.0 - - + -
581A THR* 4.2 14.8 - - + -
582A THR* 3.6 26.5 - - + -
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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