Contacts of the helix formed by residues 523 - 530 (chain B) in PDB entry 1JPP
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 ASN 523 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482B GLN 3.7 13.8 + - - -
486B ARG* 2.9 39.5 + - - +
491B LEU* 4.2 10.1 - - + +
517B LEU* 3.1 28.9 + - - +
518B ALA* 5.0 1.3 - - - -
520B CYS* 3.0 31.3 + - - +
521B PRO 2.6 7.3 + - - -
522B ALA* 1.3 73.8 - - - +
524B HIS* 1.3 62.7 + - - +
526B PRO* 3.4 7.6 - - - -
527B LEU* 3.3 38.1 + - + +
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Residues in contact with HIS 524 (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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518B ALA* 3.2 27.3 + - - -
519B LEU 5.4 0.8 - - - -
520B CYS 4.0 0.4 + - - -
521B PRO* 2.8 43.7 + - + +
523B ASN* 1.3 79.1 - - - +
525B ALA* 1.3 63.0 + - - +
527B LEU* 4.3 2.1 - - - +
528B ARG* 3.7 16.9 + - - +
579B ILE 4.1 17.7 + - - -
580B LEU* 4.5 21.6 + - - +
582B ARG* 4.6 17.3 - - + +
583B ASP* 4.2 27.1 - - + +
586B ASN* 4.0 12.6 + - - +
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Residues in contact with ALA 525 (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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521B PRO 4.6 0.6 + - - -
522B ALA 5.1 0.2 - - - -
524B HIS* 1.3 75.2 - - - +
526B PRO* 1.3 75.0 - - + +
528B ARG* 3.2 36.5 + - - +
529B GLU* 3.2 24.4 + - - +
583B ASP* 5.7 1.1 + - - +
585B HIS* 6.4 0.4 - - + -
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Residues in contact with PRO 526 (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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486B ARG* 4.2 9.6 - - + -
491B LEU* 3.4 25.6 - - + -
522B ALA 3.4 18.8 - - - +
523B ASN* 3.4 15.9 - - - +
525B ALA* 1.3 96.6 - - + +
527B LEU* 1.3 61.3 + - - +
528B ARG 3.2 0.5 + - - -
529B GLU* 3.3 14.4 + - - +
530B GLN* 3.2 26.1 + - - +
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Residues in contact with LEU 527 (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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491B LEU* 4.4 26.2 - - + +
494B VAL* 6.1 1.3 - - + -
495B VAL* 4.4 20.4 - - + -
514B ILE* 4.6 24.0 - - + -
517B LEU* 4.7 10.5 - - + -
518B ALA* 4.5 19.1 - - + +
523B ASN* 3.3 27.3 + - + +
524B HIS 4.3 2.7 - - - +
526B PRO* 1.3 78.5 - - - +
528B ARG* 1.3 62.4 + - - +
530B GLN* 3.6 6.5 + - + +
531B GLY 3.5 4.3 + - - -
532B ALA* 3.5 28.5 + - + +
533B ILE* 6.1 0.4 - - - -
580B LEU* 4.4 22.9 - - + -
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Residues in contact with ARG 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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524B HIS 3.7 4.8 + - - +
525B ALA* 3.2 37.2 + - - +
526B PRO 3.1 0.6 - - - -
527B LEU* 1.3 79.6 - - - +
529B GLU* 1.3 77.3 + - - +
531B GLY* 2.7 27.7 + - - -
532B ALA 4.1 2.1 + - - +
533B ILE* 4.4 17.7 - - + +
534B PRO* 5.5 0.7 - - - +
580B LEU* 5.8 1.5 - - + +
583B ASP* 4.4 3.0 + - - -
585B HIS* 3.7 35.0 - - - +
586B ASN* 3.5 26.1 + - - +
589B VAL* 4.6 20.2 - - + -
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Residues in contact with GLU 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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525B ALA* 3.2 20.5 - - - +
526B PRO* 3.3 15.1 + - - +
528B ARG* 1.3 90.2 + - - +
530B GLN* 1.3 66.9 + - - +
531B GLY* 2.9 6.5 + - - -
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Residues in contact with GLN 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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491B LEU* 4.3 21.3 - - + +
492B PRO* 3.8 33.6 - - + +
495B VAL* 4.2 24.7 - - + +
526B PRO 3.2 14.4 + - - +
527B LEU* 3.9 9.6 - - + +
528B ARG 3.2 0.8 - - - -
529B GLU* 1.3 80.3 - - - +
531B GLY* 1.3 63.8 + - - +
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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