Contacts of the helix formed by residues 527 - 539 (chain A) in PDB entry 1JSC
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 TYR 527 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A HIS* 3.7 25.8 - + + -
147A GLU* 3.7 25.2 - - + +
151A ARG* 3.3 32.0 + - - -
176A ASP* 3.7 19.7 - - - -
182A ILE* 4.2 2.1 - - - +
495A THR 3.8 13.5 - - - +
496A GLY* 5.0 1.5 - - - -
497A VAL* 5.3 0.2 - - + -
517A ILE* 3.6 19.0 - - + +
518A THR 3.8 0.9 - - - -
519A SER* 3.7 33.7 - - - -
524A THR* 3.1 17.9 + - - +
525A MET 3.3 2.2 + - - -
526A GLY* 1.3 76.3 - - - +
528A GLY* 1.3 65.4 + - - +
530A PRO* 3.3 6.2 - - - +
531A ALA* 3.0 45.5 + - + +
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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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494A THR* 3.0 14.1 + - - -
495A THR 3.2 22.4 + - - -
496A GLY* 4.2 2.4 - - - -
526A GLY 3.4 1.8 - - - -
527A TYR* 1.3 78.3 - - - +
529A LEU* 1.3 55.5 + - - +
532A ALA* 2.9 26.2 + - - +
546A ASP* 3.4 20.9 - - - -
548A ASP* 4.1 4.2 + - - -
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Residues in contact with LEU 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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526A GLY 4.3 1.4 + - - -
528A GLY* 1.3 71.9 - - - +
530A PRO* 1.3 72.5 - - + +
532A ALA* 3.1 5.6 + - - +
533A ILE* 3.0 40.0 + - + +
546A ASP* 3.4 12.5 + - - +
548A ASP* 3.9 3.9 + - - +
553A PHE* 4.0 16.8 - - + -
556A THR* 3.8 20.2 - - - +
557A LEU* 4.1 3.4 - - - -
559A GLU* 3.9 7.9 - - + +
560A LEU* 3.5 45.1 - - + +
563A ALA* 5.1 0.7 - - + -
570A VAL* 4.6 3.8 - - + -
572A ILE* 3.5 27.1 - - + -
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Residues in contact with PRO 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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141A GLY* 3.9 12.3 - - - +
144A HIS* 3.7 24.9 - - + -
145A MET* 3.2 30.0 - - + +
526A GLY 3.2 27.6 - - - +
527A TYR 3.3 7.2 - - - +
529A LEU* 1.3 92.7 - - + +
531A ALA* 1.3 60.2 + - - +
533A ILE* 3.2 8.5 + - + +
534A GLY 3.0 18.4 + - - -
556A THR* 3.7 11.7 - - + +
559A GLU* 4.5 7.4 - - + -
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Residues in contact with ALA 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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144A HIS 3.5 15.8 + - - +
148A GLY* 3.4 13.1 - - - -
494A THR* 4.0 10.0 - - + +
517A ILE* 4.3 0.7 - - + -
527A TYR* 3.0 52.1 + - + +
528A GLY 3.9 2.2 - - - +
530A PRO* 1.3 77.1 - - - +
532A ALA* 1.3 57.4 + - - +
534A GLY 3.4 0.5 + - - -
535A ALA* 2.9 29.5 + - - +
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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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494A THR* 3.4 20.1 - - - +
528A GLY 2.9 18.9 + - - +
529A LEU* 3.1 6.0 + - - +
531A ALA* 1.3 76.1 - - - +
533A ILE* 1.3 58.9 + - - +
535A ALA* 3.6 1.2 - - - +
536A GLN* 2.9 31.0 + - - +
544A VAL* 3.7 17.5 - - + +
546A ASP* 4.1 11.9 - - + +
570A VAL* 3.6 14.6 - - + +
572A ILE* 5.1 0.7 - - + -
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Residues in contact with ILE 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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134A VAL* 4.9 2.5 - - + -
145A MET* 3.9 19.1 - - - -
529A LEU* 3.0 33.1 + - + +
530A PRO* 3.2 11.0 + - + +
532A ALA* 1.3 76.6 - - - +
534A GLY* 1.3 58.9 + - - +
536A GLN* 3.3 3.6 + - - +
537A VAL* 3.0 32.9 + - + +
559A GLU* 3.6 32.1 - - + +
562A SER* 4.5 4.9 - - - +
563A ALA* 3.9 18.6 - - + +
566A ALA* 4.9 9.2 - - + -
568A THR* 3.8 23.7 - - + +
570A VAL* 4.1 10.1 - - + -
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Residues in contact with GLY 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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111A PHE* 4.2 14.1 - - - -
145A MET* 3.3 25.5 - - - +
149A TYR* 3.5 17.5 - - - +
530A PRO 3.0 11.1 + - - -
531A ALA 3.8 0.4 - - - -
533A ILE* 1.3 73.7 - - - +
535A ALA* 1.3 65.4 + - - +
537A VAL* 3.3 4.4 + - - +
538A ALA 3.1 16.8 + - - -
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Residues in contact with ALA 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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148A GLY 3.8 8.7 - - - +
152A ALA* 3.9 8.5 - - + +
492A ILE* 4.2 13.0 - - + +
494A THR* 4.7 0.9 - - + -
517A ILE* 3.9 26.7 - - + -
531A ALA 2.9 18.1 + - - +
532A ALA* 3.3 8.5 + - - +
534A GLY* 1.3 75.9 - - - +
536A GLN* 1.3 58.5 + - - +
538A ALA* 3.1 4.6 + - - +
539A LYS* 2.9 31.5 + - - +
544A VAL* 4.4 4.9 - - + -
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Residues in contact with GLN 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 2.9 17.4 + - - +
533A ILE 3.5 5.4 - - - +
534A GLY 3.2 0.2 - - - -
535A ALA* 1.3 77.6 - - - +
537A VAL* 1.3 61.9 + - - +
539A LYS 3.0 45.3 - - - +
540A PRO* 3.2 14.8 - - + +
542A SER 3.1 16.7 + - - +
543A LEU* 5.1 0.2 - - - +
544A VAL* 3.5 25.6 - - + +
568A THR* 3.5 26.9 - - + -
569A PRO* 3.5 44.5 + - + +
570A VAL* 3.9 4.7 - - + +
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Residues in contact with VAL 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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109A THR* 4.0 25.9 + - + +
111A PHE* 4.7 2.2 - - + -
132A ASN* 3.8 24.5 - - - +
134A VAL* 4.3 17.5 - - + -
149A TYR* 4.5 4.2 - - + -
533A ILE* 3.0 25.4 + - + +
534A GLY* 3.6 10.8 - - - +
535A ALA 3.2 0.2 - - - -
536A GLN* 1.3 76.5 - - - +
538A ALA* 1.3 60.1 + - - +
540A PRO* 3.8 12.9 - - - +
566A ALA* 5.1 4.0 - - + +
568A THR* 3.6 18.2 - - + -
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Residues in contact with ALA 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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149A TYR* 3.5 44.6 - - + +
152A ALA* 4.3 7.4 - - + -
153A SER* 3.9 13.1 - - - +
534A GLY 3.1 7.4 + - - +
535A ALA 3.1 9.9 + - - +
537A VAL* 1.3 80.5 - - - +
539A LYS* 1.3 68.3 + - + +
540A PRO* 3.4 7.0 - - - +
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Residues in contact with LYS 539 (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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152A ALA* 3.4 26.7 - - + +
153A SER* 4.7 7.2 + - - +
490A HIS* 5.1 8.1 - - + -
492A ILE* 3.8 17.9 - - + -
535A ALA 2.9 11.2 + - - +
536A GLN* 3.0 15.7 - - - +
538A ALA* 1.3 84.5 - - + +
540A PRO* 1.3 66.5 - - - +
541A GLU 3.2 2.5 - - - -
542A SER* 3.0 33.6 + - - +
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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