Contacts of the helix formed by residues 531 - 547 (chain B) in PDB entry 1JPW
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 GLY 531 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495B VAL* 4.0 4.9 - - - +
499B HIS* 4.7 3.9 + - - -
528B ARG 2.7 13.0 + - - -
529B GLU 3.3 1.4 - - - -
530B GLN* 1.3 80.8 - - - +
532B ALA* 1.3 62.8 + - - +
533B ILE 3.6 1.6 - - - -
534B PRO* 3.7 17.9 - - - +
535B ARG* 3.9 14.4 + - - +
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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
----------------------------------------------------------
495B VAL* 3.9 24.2 - - + +
498B LEU* 4.9 0.8 - - - +
514B ILE* 5.0 8.3 - - + -
527B LEU* 3.1 33.0 + - + +
528B ARG 3.9 0.6 + - - -
530B GLN 3.6 1.0 - - - -
531B GLY* 1.3 75.4 - - - +
533B ILE* 1.3 68.1 + - - +
535B ARG* 3.3 4.2 + - - +
536B LEU* 3.0 37.0 + - + +
580B LEU* 4.9 4.7 - - + -
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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
----------------------------------------------------------
528B ARG* 3.9 23.1 - - + -
532B ALA* 1.3 75.0 - - + +
534B PRO* 1.3 71.6 - - + +
536B LEU* 3.0 18.2 + - - +
537B VAL* 3.0 22.1 + - + +
577B LEU* 4.2 9.2 - - + -
580B LEU* 4.3 17.0 - - + -
586B ASN* 3.7 36.1 - - + +
589B VAL* 3.7 33.7 - - + -
590B ILE* 3.8 24.7 - - + +
593B LEU* 4.5 1.1 - - + -
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Residues in contact with PRO 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ARG 5.5 1.3 - - - +
531B GLY* 3.7 17.7 - - - +
532B ALA 3.6 2.7 - - - -
533B ILE* 1.3 96.2 - - + +
535B ARG* 1.3 59.4 + - - +
537B VAL* 3.5 2.8 + - - +
538B GLN* 3.1 27.4 + - - +
589B VAL* 4.9 7.2 - - + -
593B LEU* 3.7 26.2 - - + +
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Residues in contact with ARG 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 5.6 5.4 + - - -
498B LEU* 3.0 43.4 + - + -
499B HIS* 3.5 37.6 + - + +
500B PRO* 4.0 19.1 - - - +
507B ILE* 4.9 4.8 - - - +
531B GLY 3.9 6.4 + - - +
532B ALA* 3.3 7.5 + - - +
533B ILE 3.2 0.8 - - - -
534B PRO* 1.3 77.5 - - - +
536B LEU* 1.3 65.3 + - - +
538B GLN* 3.5 16.0 + - - +
539B LEU* 3.1 49.4 + - + +
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Residues in contact with LEU 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B LEU* 4.1 21.1 - - + -
511B VAL* 4.5 12.1 - - + -
514B ILE* 4.2 16.8 - - + -
532B ALA 3.0 21.8 + - - +
533B ILE 3.0 6.3 + - - +
535B ARG* 1.3 76.1 - - - +
537B VAL* 1.3 63.3 + - - +
539B LEU* 3.3 3.2 + - + -
540B LEU* 3.0 22.2 + - - +
573B CYS* 3.6 27.0 - - + +
576B ALA* 3.9 30.1 - - + -
577B LEU* 4.1 17.9 - - + -
580B LEU* 4.0 23.8 - - + -
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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
----------------------------------------------------------
533B ILE* 3.0 17.0 + - + +
534B PRO 3.7 7.0 - - - +
535B ARG 3.3 0.2 - - - -
536B LEU* 1.3 77.0 - - - +
538B GLN* 1.3 61.4 + - - +
540B LEU* 3.0 14.7 - - + +
541B VAL* 3.0 40.5 + - + +
577B LEU* 4.1 20.2 - - + -
590B ILE* 5.2 2.0 - - + -
593B LEU* 3.9 29.4 - - + +
595B THR* 3.6 31.4 - - + -
598B LEU* 5.6 0.7 - - + -
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Residues in contact with GLN 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B PRO 3.1 19.1 + - - +
535B ARG* 3.5 19.5 + - - +
536B LEU 3.3 0.2 - - - -
537B VAL* 1.3 82.3 - - - +
539B LEU* 1.3 61.7 + - - +
541B VAL* 3.4 22.7 + - - +
542B ARG* 3.2 23.2 + - - +
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Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B LEU* 4.0 18.4 - - + +
504B TRP* 4.2 21.7 - - + -
507B ILE* 3.5 31.2 - - + -
511B VAL* 5.0 1.6 - - + -
535B ARG* 3.1 66.5 + - + +
536B LEU* 3.8 5.2 - - + +
538B GLN* 1.3 73.7 - - - +
540B LEU* 1.3 65.4 + - - +
542B ARG* 3.9 6.5 - - + +
543B ALA* 3.0 25.3 + - - +
569B ILE* 4.2 3.0 - - + +
573B CYS* 4.0 15.0 - - - -
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Residues in contact with LEU 540 (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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536B LEU 3.0 12.7 + - - +
537B VAL* 3.0 15.7 - - + +
539B LEU* 1.3 77.9 - - - +
541B VAL* 1.3 52.6 + - - +
543B ALA* 3.1 6.9 + - - +
544B HIS* 2.8 36.7 + - + +
570B VAL* 4.0 24.6 - - + +
573B CYS* 3.9 10.3 - - + -
574B THR* 3.2 21.8 - - - +
577B LEU* 3.9 16.6 - - + -
595B THR* 5.5 0.2 - - + -
598B LEU* 3.6 24.0 - - + -
599B PHE* 3.7 29.6 - - + -
602B LEU* 4.4 6.3 - - + -
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Residues in contact with VAL 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B VAL* 3.0 20.8 + - + +
538B GLN* 3.5 29.2 - - - +
539B LEU 3.3 0.2 - - - -
540B LEU* 1.3 74.5 - - - +
542B ARG* 1.3 65.3 + - - +
544B HIS* 3.0 14.6 + - - +
545B GLN* 3.1 38.9 + - + +
598B LEU* 4.2 22.9 - - + -
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Residues in contact with ARG 542 (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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306A TYR* 5.1 17.4 + - - -
504B TRP* 4.5 19.7 - - + -
538B GLN 3.2 14.0 + - - +
539B LEU* 3.9 8.7 - - + +
541B VAL* 1.3 79.8 - - - +
543B ALA* 1.3 61.9 + - - +
545B GLN* 3.7 24.9 + - - +
546B ASP* 2.5 48.8 + - - +
549B ARG* 5.9 2.4 - - - +
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Residues in contact with ALA 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B TRP* 5.3 1.1 - - + -
539B LEU 3.0 19.6 + - - +
540B LEU 3.3 5.4 - - - +
541B VAL 3.1 0.2 - - - -
542B ARG* 1.3 79.5 - - - +
544B HIS* 1.3 62.3 + - - +
546B ASP* 3.1 20.9 + - - +
547B THR* 3.4 11.6 + - - -
566B MET* 3.7 19.6 - - + +
569B ILE* 4.0 15.9 - - + -
570B VAL* 3.3 21.3 - - + +
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Residues in contact with HIS 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 2.8 18.0 + - + +
541B VAL* 3.0 10.7 + - - +
543B ALA* 1.3 70.9 - - - +
545B GLN* 1.3 68.8 + - + +
547B THR* 3.3 7.8 + - - -
548B GLN* 3.3 43.0 + - + +
570B VAL* 3.8 11.3 - - + +
598B LEU* 3.7 29.4 - - + +
601B GLN* 4.6 17.4 - - + +
602B LEU* 4.0 29.9 - - + +
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Residues in contact with GLN 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B VAL* 3.1 27.6 + - + +
542B ARG* 3.8 35.3 + - - +
544B HIS* 1.3 79.9 - - + +
546B ASP* 1.3 58.4 + - - +
548B GLN* 2.9 29.9 + - + +
549B ARG* 3.3 22.7 + - - +
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Residues in contact with ASP 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B TRP* 5.6 0.3 + - - -
542B ARG* 2.5 45.1 + - - +
543B ALA 3.1 14.4 - - - +
544B HIS 3.1 0.4 - - - -
545B GLN* 1.3 81.4 - - - +
547B THR* 1.3 57.7 + - - +
548B GLN 3.3 0.5 + - - -
549B ARG* 4.0 12.3 + - - +
561B VAL* 4.5 8.5 - - - +
566B MET* 2.8 38.8 - - + +
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Residues in contact with THR 547 (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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543B ALA 3.4 9.7 + - - -
544B HIS* 3.3 10.3 + - - -
546B ASP* 1.3 76.4 - - - +
548B GLN* 1.3 63.9 - - - +
549B ARG 4.0 5.1 - - - +
566B MET* 4.1 8.1 + - - +
567B GLU* 3.0 46.6 + - + +
570B VAL* 4.9 2.4 - - - +
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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
------------------------------------------------------------
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