Contacts of the helix formed by residues 524 - 536 (chain A) in PDB entry 2PTM
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 SER 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523A VAL* 1.3 81.2 - - - +
525A GLU* 1.3 63.5 + - - +
526A SER* 3.5 10.1 + - - -
527A ILE* 3.0 33.7 + - - +
528A ARG* 3.0 21.3 + - - +
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Residues in contact with GLU 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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524A SER* 1.3 74.7 - - - +
526A SER* 1.3 56.9 + - - +
528A ARG* 3.2 31.0 + - + +
529A GLN* 2.9 52.5 + - + +
556A ARG* 4.6 12.3 + - - -
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Residues in contact with SER 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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524A SER* 3.1 10.1 + - - -
525A GLU* 1.3 76.1 - - - +
527A ILE* 1.3 62.0 + - - +
529A GLN* 3.2 14.1 + - - +
530A ASP* 2.9 40.6 + - - +
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Residues in contact with ILE 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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519A ILE* 6.3 0.7 - - + -
523A VAL* 3.5 35.9 - - + -
524A SER* 3.0 26.5 + - - +
526A SER* 1.3 75.9 - - - +
528A ARG* 1.3 57.4 + - - +
530A ASP* 3.2 9.1 + - - +
531A VAL* 2.8 50.4 + - + +
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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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520A PHE* 3.0 65.6 + - + +
521A ARG* 4.4 7.0 + - - +
523A VAL* 2.9 30.1 + - + -
524A SER 3.0 8.2 + - - +
525A GLU* 3.3 41.3 - - + +
527A ILE* 1.3 78.9 - - - +
529A GLN* 1.3 57.8 + - + +
531A VAL* 4.8 0.2 - - - -
532A ALA* 3.0 31.0 + - - +
559A THR* 4.5 5.3 - - + +
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Residues in contact with GLN 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 GLU* 2.9 46.5 + - + +
526A SER* 3.2 13.8 + - - +
528A ARG* 1.3 73.7 - - + +
530A ASP* 1.3 63.4 + - - +
532A ALA* 4.0 0.5 - - - +
533A ASN* 2.8 39.5 + - - +
555A THR* 3.6 32.1 - - + +
556A ARG* 5.7 4.4 - - - +
559A THR* 3.9 17.4 - - + +
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Residues in contact with ASP 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 SER* 2.9 26.8 + - - +
527A ILE* 3.6 9.3 - - - +
529A GLN* 1.3 79.2 - - - +
531A VAL* 1.3 59.1 + - + +
533A ASN* 3.8 6.5 + - - +
534A TYR* 3.0 28.4 + - - +
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Residues in contact with VAL 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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516A GLU* 5.7 0.2 - - + -
520A PHE* 3.4 33.7 - - + -
527A ILE* 2.8 39.1 + - + +
530A ASP* 1.3 72.8 - - + +
532A ALA* 1.3 65.1 + - - +
534A TYR* 3.2 4.2 + - - -
535A ASN* 2.9 40.5 + - - +
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Residues in contact with ALA 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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520A PHE* 4.0 13.4 - - + -
528A ARG 3.0 19.6 + - - +
529A GLN 4.0 2.2 - - - +
531A VAL* 1.3 76.4 - - - +
533A ASN* 1.3 62.7 + - - +
535A ASN* 3.9 4.4 - - - +
536A CYS* 3.0 31.7 + - - +
558A VAL* 3.8 32.1 - - + +
559A THR* 4.2 9.0 - - + -
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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 GLN* 2.8 28.7 + - - +
530A ASP* 3.8 7.0 + - - +
532A ALA* 1.3 78.0 - - - +
534A TYR* 1.3 60.6 + - - +
536A CYS* 3.7 1.7 - - - -
537A ARG* 3.1 23.6 + - - +
540A VAL* 5.6 1.7 - - - +
554A VAL* 4.2 13.5 - - - +
555A THR* 3.2 31.0 + - - +
558A VAL* 3.7 18.3 - - - +
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Residues in contact with TYR 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 ASP 3.0 17.5 + - - +
531A VAL* 3.2 5.4 + - - +
533A ASN* 1.3 74.6 - - - +
535A ASN* 1.3 73.9 + - - +
537A ARG* 2.8 78.4 + - - +
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Residues in contact with ASN 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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516A GLU* 3.3 24.5 + - - -
520A PHE* 4.9 0.8 - - - -
531A VAL* 2.9 36.2 + - - +
532A ALA* 4.1 4.7 - - - +
534A TYR* 1.3 87.2 - - - +
536A CYS* 1.3 63.4 + - - +
537A ARG* 3.4 8.1 + - - +
538A ASP* 5.0 2.3 + - - +
586A GLN* 4.5 13.2 + - - -
633A PHE* 5.2 3.8 - - + -
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Residues in contact with CYS 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 ALA* 3.0 21.3 + - - +
533A ASN 3.7 2.9 - - - +
535A ASN* 1.3 80.3 - - - +
537A ARG* 1.3 63.4 + - - +
538A ASP 3.4 2.9 - - - -
539A LEU* 3.2 13.0 + - + +
540A VAL* 2.9 25.4 + - + +
558A VAL* 3.7 34.5 - - + -
561A LEU* 4.3 12.8 - - - -
586A GLN* 5.7 0.4 - - - +
633A PHE* 4.2 27.4 - - - -
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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