Contacts of the helix formed by residues 527 - 536 (chain A) in PDB entry 3P1X
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 527 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A LYS* 1.3 78.7 - - + +
528A PRO* 1.3 64.5 - - - +
529A VAL* 3.1 14.9 + - - +
530A MSE 2.9 47.1 + - + +
531A GLU* 2.8 31.3 + - - +
578A ALA* 6.1 1.8 - - - +
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Residues in contact with PRO 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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526A LYS 3.4 9.1 - - - +
527A ASN* 1.3 86.9 - - + +
529A VAL* 1.3 63.1 + - - +
531A GLU* 4.6 1.1 - - + -
532A LEU* 2.9 27.2 + - - +
578A ALA* 3.4 40.2 - - + +
581A ALA* 3.6 9.1 - - + +
582A LEU* 3.9 17.7 - - + +
585A LEU* 3.6 13.6 - - + +
594A LEU* 4.1 18.1 - - + -
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Residues in contact with VAL 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ASN* 3.1 11.0 + - - +
528A PRO* 1.3 76.1 - - - +
530A MSE 1.3 64.6 + - + +
532A LEU* 4.0 1.4 - - - +
533A ASN* 3.0 25.3 + - + +
541A TYR* 3.9 22.1 + - + +
574A LYS 5.7 0.4 - - - +
577A LYS* 3.7 37.7 - - + +
578A ALA* 4.2 9.4 - - + -
581A ALA* 3.8 16.4 - - + -
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Residues in contact with MSE 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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527A ASN* 2.9 40.8 + - + +
529A VAL* 1.3 78.4 - - + +
531A GLU* 1.3 67.0 + - - +
533A ASN* 3.3 9.6 + - - +
534A GLU* 3.2 25.2 + - - +
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Residues in contact with GLU 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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525A GLY* 3.1 36.1 + - - -
526A LYS 4.0 5.4 + - - +
527A ASN 2.8 22.3 + - - +
528A PRO* 3.9 3.6 - - + +
530A MSE 1.3 75.9 - - - +
532A LEU* 1.3 65.2 + - - +
534A GLU* 3.1 27.9 + - - +
535A LYS* 3.6 15.8 + - - +
585A LEU* 3.9 17.4 - - + +
592A THR* 3.9 23.8 - - + +
593A PRO* 4.7 1.9 - - - +
594A LEU* 6.1 2.2 - - + -
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Residues in contact with LEU 532 (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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528A PRO 2.9 17.8 + - - +
529A VAL 4.0 2.9 - - - +
531A GLU* 1.3 76.7 - - - +
533A ASN* 1.3 51.3 + - - +
535A LYS* 2.8 8.0 + - + +
536A ARG* 2.8 34.3 + - + +
539A LEU* 3.4 29.6 - - + -
541A TYR* 3.6 15.9 - - + +
559A VAL* 4.7 2.0 - - + -
561A VAL* 4.2 9.4 - - + -
581A ALA* 4.1 10.5 - - + -
584A ALA* 3.8 29.6 - - + -
585A LEU* 3.7 26.4 - - + +
589A PHE* 4.2 20.6 - - + -
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Residues in contact with ASN 533 (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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529A VAL* 3.0 21.7 + - + +
530A MSE 3.3 10.0 - - - +
532A LEU* 1.3 78.2 - - - +
534A GLU* 1.3 67.2 + - - +
535A LYS 3.3 0.5 + - - -
536A ARG 3.3 20.6 + - - +
537A ARG* 3.7 26.6 + - - +
538A GLY* 4.0 6.7 - - - +
539A LEU* 5.2 3.7 - - - +
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Residues in contact with GLU 534 (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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530A MSE 3.2 14.9 + - - +
531A GLU* 3.1 24.0 + - - +
532A LEU 3.1 0.2 - - - -
533A ASN* 1.3 84.6 - - - +
535A LYS* 1.3 69.1 + - - +
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Residues in contact with LYS 535 (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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531A GLU* 3.9 15.7 + - - +
532A LEU* 2.8 8.4 + - - +
533A ASN 4.2 0.2 - - - -
534A GLU* 1.3 89.9 - - - +
536A ARG* 1.3 77.7 + - + +
537A ARG 4.3 0.2 - - - -
585A LEU* 5.1 0.9 - - + -
589A PHE* 3.6 56.3 - - + -
592A THR* 3.9 21.7 + - - +
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Residues in contact with ARG 536 (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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532A LEU* 2.8 9.8 + - + +
533A ASN* 3.3 20.5 + - - -
535A LYS* 1.3 98.1 + - + +
537A ARG* 1.3 64.0 + - - +
539A LEU* 3.5 34.3 - - + +
561A VAL* 4.1 15.7 - - + +
562A ASP* 3.0 40.7 + - - -
588A LEU* 5.5 0.8 - - - +
589A PHE* 3.7 27.9 - - + -
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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