Contacts of the helix formed by residues 527 - 538 (chain A) in PDB entry 2PME
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 LEU 527 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LYS* 5.7 2.5 - - - -
107A ILE* 4.5 18.4 - - + +
108A ILE* 4.1 23.1 - - + -
111A TRP* 5.1 6.3 - - + -
272A ILE* 4.7 3.4 - - + -
293A THR* 3.3 45.0 + - + +
294A MET 4.2 8.7 - - - +
295A ALA* 4.3 9.9 - - + +
362A TYR* 4.8 4.7 - - - +
525A PHE* 3.9 18.4 - - + +
526A GLY* 1.3 69.7 - - - -
528A GLY* 1.3 60.3 + - - +
529A ARG 3.3 0.2 - - - -
530A ILE* 3.7 21.6 - - + +
531A MET* 2.9 41.2 + - + +
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Residues in contact with GLY 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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96A PHE* 5.1 7.0 - - - -
286A LEU* 4.1 22.4 - - - +
292A PHE* 6.0 3.4 - - - +
293A THR* 4.4 5.3 + - - +
526A GLY 3.4 0.4 - - - -
527A LEU* 1.3 77.0 - - - +
529A ARG* 1.3 57.5 + - - +
531A MET* 3.3 10.7 + - - +
532A TYR* 2.8 29.7 + - - +
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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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277A ARG* 6.1 1.0 - - - +
286A LEU 4.1 13.7 + - - +
287A ILE* 2.8 46.4 + - + +
288A ARG* 4.4 9.7 - - - +
402A ILE* 4.6 16.0 - - + +
403A GLU* 3.0 41.5 + - - +
404A ILE* 3.9 13.9 - - + +
526A GLY* 3.3 12.6 + - - +
528A GLY* 1.3 73.4 - - - +
530A ILE* 1.3 61.1 + - - +
532A TYR* 3.2 6.9 + - - +
533A THR* 2.6 35.4 + - - -
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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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107A ILE* 4.8 7.6 - - + -
362A TYR* 4.3 9.2 - - + -
363A LEU* 4.1 22.0 - - + -
366A VAL* 4.4 18.6 - - + -
368A ILE* 4.3 7.1 - - + +
404A ILE* 4.1 18.1 - - + +
405A VAL* 3.9 20.0 - - + -
525A PHE* 4.0 21.3 - - + -
526A GLY 3.0 23.1 + - - +
527A LEU* 3.7 18.4 - - + +
529A ARG* 1.3 75.9 - - - +
531A MET* 1.3 64.2 + - - +
533A THR* 3.2 8.4 + - - -
534A VAL* 3.0 25.8 + - - +
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Residues in contact with MET 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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96A PHE* 4.0 25.1 - - + -
100A GLY* 4.4 4.3 - - - +
103A LEU* 3.5 32.1 - - + -
104A LYS* 3.7 43.5 - - + -
107A ILE* 4.5 12.3 - - + -
286A LEU* 5.6 0.9 - - + -
527A LEU* 2.9 28.5 + - + +
528A GLY* 3.5 7.9 - - - +
529A ARG 3.1 0.2 - - - -
530A ILE* 1.3 79.3 - - - +
532A TYR* 1.3 55.8 + - - +
534A VAL* 3.2 11.0 + - - +
535A PHE* 3.0 44.5 + - + -
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Residues in contact with TYR 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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67A ARG* 4.1 4.9 + - - -
70A MET* 3.4 26.2 - - + +
71A GLU* 4.2 7.7 + - - -
80A TYR* 3.4 28.3 - + - -
285A GLY* 6.2 1.8 - - - -
286A LEU* 4.5 18.2 - - + -
287A ILE* 3.8 18.4 - - + -
397A THR* 4.9 4.7 - - + -
398A SER* 4.1 1.2 + - - -
399A TYR* 3.3 34.3 + + - -
528A GLY 2.8 16.7 + - - +
529A ARG* 3.2 7.8 + - - +
531A MET* 1.3 73.4 - - - +
533A THR* 1.3 67.6 + - - +
535A PHE* 3.2 16.7 + + + +
536A GLU* 2.9 53.0 + - + +
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Residues in contact with THR 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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368A ILE* 3.9 17.7 - - + -
395A SER* 3.2 38.5 + - - +
397A THR* 4.5 5.1 - - + +
402A ILE* 4.3 5.9 - - - +
404A ILE* 3.5 8.5 - - - +
529A ARG 2.6 19.3 + - - -
530A ILE 3.3 9.0 - - - -
532A TYR* 1.3 80.9 - - - +
534A VAL* 1.3 57.0 + - - +
536A GLU* 3.3 4.1 + - - -
537A HIS* 2.9 55.3 + - + +
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Residues in contact with VAL 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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103A LEU* 5.6 1.6 - - + -
107A ILE* 4.7 1.8 - - + -
366A VAL* 3.5 46.2 - - + +
367A GLY* 4.2 6.5 - - - -
368A ILE* 4.1 13.5 - - + -
530A ILE* 3.0 18.7 + - + +
531A MET* 3.2 10.7 + - + +
533A THR* 1.3 73.9 - - - +
535A PHE* 1.3 62.7 + - + +
537A HIS* 3.9 3.3 - - - -
538A THR* 2.8 40.1 + - - +
553A PHE* 3.8 27.4 - - + -
557A VAL* 5.0 2.9 - - + -
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Residues in contact with PHE 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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70A MET* 3.6 15.9 - - + -
74A LEU* 3.8 15.3 - - + -
79A PHE* 3.8 23.3 - + + -
80A TYR* 3.6 34.3 - + - -
96A PHE* 5.6 0.9 - + - -
100A GLY* 5.7 1.3 - - - -
103A LEU* 3.6 27.4 - - + -
286A LEU* 4.6 3.8 - - + -
531A MET* 3.0 46.3 + - + -
532A TYR* 3.2 20.2 + + - +
534A VAL* 1.3 76.5 - - - +
536A GLU* 1.3 55.8 + - - +
539A PHE* 3.0 34.0 + - - +
551A PHE* 3.3 10.3 - + + -
553A PHE* 3.8 13.9 - + - -
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Residues in contact with GLU 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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64A ILE* 5.1 1.7 - - - +
65A VAL* 3.6 40.6 - - + +
67A ARG* 4.7 0.3 + - - +
70A MET* 3.6 21.8 - - + +
372A LYS* 5.1 3.8 + - - -
396A LYS 4.7 0.2 - - - +
397A THR* 3.3 13.2 - - + -
398A SER* 2.7 43.4 + - - -
532A TYR* 2.9 46.0 + - + +
533A THR* 3.8 5.2 - - - +
534A VAL 3.2 0.4 - - - -
535A PHE* 1.3 74.4 - - - +
537A HIS* 1.3 67.5 + - + +
538A THR 3.2 5.5 + - - -
539A PHE 4.2 3.7 + - - +
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Residues in contact with HIS 537 (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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367A GLY 3.9 16.6 - - - +
368A ILE* 3.6 12.7 - - + +
369A SER* 3.1 35.2 + - - +
372A LYS* 3.4 47.6 + - + +
395A SER* 4.3 0.2 - - - -
396A LYS 3.0 24.6 + - - -
397A THR* 4.8 0.6 - - + +
533A THR* 2.9 41.3 + - + +
534A VAL 3.4 1.1 + - - +
536A GLU* 1.3 87.1 - - + +
538A THR* 1.3 59.7 + - - +
539A PHE 5.3 0.2 - - - -
540A HIS* 4.4 12.3 + - - -
552A SER* 4.7 0.9 + - - -
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Residues in contact with THR 538 (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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367A GLY* 3.9 13.3 + - - -
534A VAL* 2.8 23.3 + - - +
536A GLU 3.2 0.2 - - - -
537A HIS* 1.3 82.7 + - - +
539A PHE* 1.3 65.6 + - - +
540A HIS* 3.1 7.8 + - - -
551A PHE* 3.5 19.4 - - + -
552A SER* 2.9 62.8 + - - +
553A PHE* 3.5 12.5 + - + +
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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