Contacts of the helix formed by residues 583 - 592 (chain A) 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 ASP 583 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A HIS* 4.2 23.1 - - + +
525A ALA* 5.6 1.6 + - - +
528A ARG* 4.9 3.9 + - - -
580A LEU 3.2 2.5 + - - +
581A ALA 3.2 0.4 - - - -
582A ARG* 1.3 79.7 - - - +
584A VAL* 1.3 68.5 + - - +
585A HIS* 2.7 54.0 + - - +
586A ASN* 3.1 33.2 + - - +
587A ARG* 3.3 12.2 + - - +
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Residues in contact with VAL 584 (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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582A ARG 4.1 0.6 + - - -
583A ASP* 1.3 70.3 - - - +
585A HIS* 1.3 94.9 + - + +
587A ARG* 2.9 45.4 + - + +
588A ILE* 3.2 26.4 + - + +
624A ASP* 5.5 2.9 - - - +
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Residues in contact with HIS 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ARG* 3.7 29.8 - - - +
583A ASP* 2.7 34.9 + - - +
584A VAL* 1.3 92.0 - - + +
586A ASN* 1.3 59.6 + - - +
588A ILE* 3.3 20.8 + - - +
589A VAL* 3.2 20.1 + - - +
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Residues in contact with ASN 586 (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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524A HIS* 4.2 15.7 + - - +
528A ARG* 3.4 33.8 + - - +
533A ILE* 3.7 20.0 - - + +
580A LEU* 3.0 38.4 + - - +
583A ASP* 3.1 27.6 + - - +
585A HIS* 1.3 74.7 - - - +
587A ARG* 1.3 57.7 + - - +
589A VAL* 3.2 5.5 + - - +
590A ILE* 2.9 37.9 + - + +
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Residues in contact with ARG 587 (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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581A ALA* 3.0 36.3 + - - +
582A ARG* 3.7 9.3 + - - +
583A ASP 3.6 3.5 - - - +
584A VAL* 2.9 45.6 + - + +
586A ASN* 1.3 76.5 - - - +
588A ILE* 1.3 63.7 + - + +
590A ILE* 4.4 2.7 - - - -
591A ARG* 3.0 28.6 + - - +
620A GLU* 3.8 19.7 + - - -
621A LEU* 3.7 28.9 - - + +
623A GLN* 3.2 32.1 + - - +
624A ASP* 3.7 21.4 + - - +
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Residues in contact with ILE 588 (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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584A VAL* 3.2 30.7 + - + +
585A HIS* 3.7 16.4 - - - +
587A ARG* 1.3 76.3 - - + +
589A VAL* 1.3 62.3 + - + +
591A ARG* 4.4 6.9 - - - +
592A GLY* 3.4 16.8 + - - -
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Residues in contact with VAL 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ARG* 4.7 14.6 - - + -
533A ILE* 4.3 22.9 - - + -
534A PRO* 5.3 5.8 - - + -
585A HIS 3.2 19.5 - - - +
586A ASN* 3.4 9.2 - - - +
587A ARG 3.1 0.4 - - - -
588A ILE* 1.3 77.6 - - + +
590A ILE* 1.3 67.7 + - - +
592A GLY* 3.2 11.6 + - - +
593A LEU* 3.5 19.7 - - + +
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Residues in contact with ILE 590 (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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533A ILE* 3.7 26.2 - - + -
537A VAL* 5.5 1.3 - - + -
577A LEU* 4.3 27.8 - - + +
580A LEU* 5.1 1.8 - - + -
581A ALA* 4.3 24.5 - - + +
586A ASN* 2.9 29.5 + - + +
587A ARG* 3.9 4.3 - - - +
589A VAL* 1.3 78.0 - - - +
591A ARG* 1.3 63.7 + - - +
593A LEU* 3.4 7.2 + - - +
595A THR* 3.2 39.7 + - + +
599A PHE* 4.3 18.4 - - + -
617A VAL* 5.4 2.9 - - + -
621A LEU* 4.6 11.9 - - + -
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Residues in contact with ARG 591 (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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587A ARG 3.0 18.8 + - - +
588A ILE* 4.4 6.7 - - - +
590A ILE* 1.3 76.9 - - - +
592A GLY* 1.3 63.2 + - - +
593A LEU 2.8 7.3 + - - -
594A ASN* 3.5 11.2 + - - +
595A THR* 4.3 8.7 + - - -
596A ILE* 4.5 25.5 - - + +
621A LEU* 4.7 15.2 - - + +
626A GLU* 5.0 14.1 + - - +
627A ALA* 5.1 16.6 - - + +
630A ALA* 4.1 21.9 - - - +
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Residues in contact with GLY 592 (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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588A ILE 3.4 11.0 + - - -
589A VAL 3.2 9.0 + - - +
591A ARG* 1.3 84.8 - - - +
593A LEU* 1.3 69.0 + - - +
594A ASN 3.7 1.6 - - - -
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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