Contacts of the helix formed by residues 527 - 539 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B HIS* 3.6 25.1 - + + -
147B GLU* 3.7 23.9 - - + +
151B ARG* 3.2 28.4 + - - -
176B ASP* 3.6 20.4 - - - -
182B ILE* 4.2 2.3 - - - +
495B THR 3.8 14.4 - - - +
496B GLY* 5.0 1.5 - - - -
497B VAL* 5.4 0.4 - - + -
517B ILE* 3.6 23.6 - - + +
518B THR* 3.8 1.3 - - - -
519B SER* 3.7 33.4 - - - -
524B THR* 3.1 18.3 + - - +
525B MET 3.3 2.0 + - - -
526B GLY* 1.3 77.5 - - - +
528B GLY* 1.3 65.1 - - - +
530B PRO* 3.3 6.2 - - - +
531B ALA* 3.0 44.2 + - + +
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Residues in contact with GLY 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B THR* 3.0 14.0 + - - -
495B THR 3.2 23.0 + - - -
496B GLY* 4.2 2.6 - - - -
526B GLY 3.4 1.6 - - - -
527B TYR* 1.3 77.8 - - - +
529B LEU* 1.3 61.9 + - - +
532B ALA* 2.9 20.4 + - - +
546B ASP* 3.3 20.9 - - - -
548B ASP* 4.1 4.0 + - - -
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526B GLY 4.3 0.8 + - - -
528B GLY* 1.3 70.9 - - - +
530B PRO* 1.3 73.4 - - + +
532B ALA* 3.1 5.6 + - - +
533B ILE* 3.0 38.7 + - + +
546B ASP* 3.4 12.5 + - - +
548B ASP* 4.0 4.3 + - - +
553B PHE* 4.0 17.0 - - + -
556B THR* 3.8 22.0 - - - +
557B LEU* 4.1 2.7 - - - -
559B GLU* 3.9 8.3 - - + +
560B LEU* 3.5 45.3 - - + +
563B ALA* 5.1 0.7 - - + -
570B VAL* 4.6 4.0 - - + -
572B ILE* 3.5 26.5 - - + -
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Residues in contact with PRO 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLY* 3.8 22.7 - - - +
144B HIS* 3.6 26.7 - - + -
145B MET* 3.2 20.4 - - + +
526B GLY 3.2 24.2 - - - +
527B TYR 3.3 7.6 - - - +
529B LEU* 1.3 95.0 - - + +
531B ALA* 1.3 59.3 + - - +
533B ILE* 3.1 8.3 + - + -
534B GLY 3.0 19.1 + - - -
556B THR* 3.6 11.7 - - - +
559B GLU* 4.5 6.7 - - + -
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Residues in contact with ALA 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B HIS 3.5 16.1 + - - +
148B GLY* 3.4 13.1 - - - -
494B THR* 4.0 9.6 - - + -
517B ILE* 4.4 0.2 - - + -
527B TYR* 3.0 52.9 + - + +
528B GLY 3.9 2.5 - - - +
530B PRO* 1.3 76.9 - - - +
532B ALA* 1.3 57.2 + - - +
534B GLY 3.4 0.5 + - - -
535B ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B THR* 3.5 20.8 - - - +
528B GLY 2.9 19.3 + - - +
529B LEU* 3.4 5.6 - - - +
531B ALA* 1.3 75.0 - - - +
533B ILE* 1.3 59.4 + - - +
535B ALA* 3.3 2.0 + - - +
536B GLN* 2.9 30.0 + - - +
544B VAL* 3.6 18.0 - - + +
546B ASP* 4.1 12.6 - - + +
570B VAL* 3.6 14.5 - - + +
572B ILE* 5.1 0.4 - - + -
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Residues in contact with ILE 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 4.8 6.5 - - + -
145B MET* 3.9 20.4 - - + -
529B LEU* 3.0 32.9 + - + +
530B PRO* 3.1 10.3 + - + +
532B ALA* 1.3 77.4 - - - +
534B GLY* 1.3 62.9 + - - +
536B GLN* 3.3 3.8 + - - +
537B VAL* 3.0 27.4 + - + +
559B GLU* 3.6 31.4 - - + +
562B SER* 4.5 4.9 - - - +
563B ALA* 3.9 18.6 - - + +
566B ALA* 4.9 4.9 - - + -
568B THR* 3.8 24.9 - - + +
570B VAL* 4.1 10.3 - - + -
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Residues in contact with GLY 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 4.2 9.9 - - - -
145B MET* 3.2 30.0 - - - +
149B TYR* 3.3 18.9 - - - +
530B PRO 3.0 10.7 + - - -
531B ALA 3.8 0.7 - - - -
533B ILE* 1.3 76.3 - - - +
535B ALA* 1.3 62.8 + - - +
537B VAL* 3.3 3.0 + - - +
538B ALA 3.1 17.2 + - - -
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Residues in contact with ALA 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLY 3.7 9.6 - - - +
152B ALA* 4.0 9.0 - - + +
492B ILE* 4.2 13.1 - - + +
494B THR* 4.7 0.4 - - + -
517B ILE* 3.9 26.7 - - + -
531B ALA 2.9 18.1 + - - +
532B ALA* 3.6 8.7 - - - +
534B GLY* 1.3 75.2 - - - +
536B GLN* 1.3 58.7 + - - +
538B ALA* 3.1 4.5 + - - +
539B LYS* 2.9 29.6 + - - +
544B VAL* 4.4 4.9 - - + -
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Residues in contact with GLN 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532B ALA 2.9 17.5 + - - +
533B ILE 3.5 5.2 - - - +
535B ALA* 1.3 78.0 - - - +
537B VAL* 1.3 61.1 + - - +
539B LYS 3.0 45.3 - - - +
540B PRO* 3.2 14.3 - - + +
542B SER 3.0 17.6 + - - +
543B LEU* 5.1 0.2 - - - +
544B VAL* 3.5 25.7 - - + +
568B THR* 3.5 27.8 - - + -
569B PRO* 3.5 43.5 + - + +
570B VAL* 3.9 3.5 - - + +
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Residues in contact with VAL 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B THR* 3.9 31.6 + - + +
111B PHE* 4.6 2.9 - - + -
132B ASN* 3.9 18.4 - - - +
134B VAL* 4.3 17.9 - - + -
149B TYR* 4.4 4.4 - - + -
533B ILE* 3.0 21.4 + - + +
534B GLY* 3.6 10.5 - - - +
535B ALA 3.3 0.2 - - - -
536B GLN* 1.3 75.2 - - - +
538B ALA* 1.3 60.2 + - - +
540B PRO* 3.8 13.1 - - - +
566B ALA* 5.1 3.6 - - + +
568B THR* 3.6 18.2 - - + -
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Residues in contact with ALA 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B TYR* 3.5 44.2 - - + +
152B ALA* 4.1 8.1 - - + -
153B SER* 3.8 15.4 - - - -
534B GLY 3.1 6.9 + - - +
535B ALA 3.1 8.8 + - - +
537B VAL* 1.3 79.9 - - - +
539B LYS* 1.3 65.9 + - - +
540B PRO* 3.5 7.0 - - - +
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Residues in contact with LYS 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ALA* 3.2 27.8 - - + +
153B SER* 4.6 6.6 + - - +
490B HIS* 5.1 7.9 - - + -
492B ILE* 3.8 19.3 - - + -
535B ALA 2.9 11.2 + - - +
536B GLN* 3.0 17.3 - - - +
538B ALA* 1.3 84.5 - - - +
540B PRO* 1.3 67.2 - - - +
541B GLU 3.2 3.1 - - - -
542B SER* 3.0 30.8 + - - +
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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