Contacts of the helix formed by residues 595 - 602 (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 THR 595 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A VAL* 4.1 26.2 - - + -
590A ILE* 3.2 31.3 + - + +
591A ARG* 4.3 6.5 + - - -
593A LEU* 3.6 19.5 - - + +
594A ASN* 1.3 76.7 - - - +
596A ILE* 1.3 71.0 + - - +
597A PRO* 3.3 3.4 - - - -
598A LEU* 2.9 22.4 + - - +
599A PHE* 3.2 37.8 + - + -
621A LEU* 5.0 0.9 - - - +
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Residues in contact with ILE 596 (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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591A ARG* 4.5 28.9 - - + +
595A THR* 1.3 81.9 + - - +
597A PRO* 1.3 70.5 - - + +
599A PHE* 3.2 9.7 + - + +
600A VAL* 3.0 36.9 + - + +
618A LEU* 5.0 4.0 - - + -
621A LEU* 4.9 14.4 - - + -
627A ALA* 4.4 5.8 - - + +
630A ALA* 4.2 19.7 - - + +
631A ILE* 3.9 34.3 - - + -
634A GLU* 4.2 13.5 - - + -
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Residues in contact with PRO 597 (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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594A ASN* 3.9 32.3 - - - +
595A THR 3.4 4.5 - - - -
596A ILE* 1.3 94.2 - - + +
598A LEU* 1.3 59.7 + - - +
600A VAL* 3.5 5.3 + - + +
601A GLN* 3.3 26.4 + - - +
634A GLU* 3.9 35.4 - - + +
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Residues in contact with LEU 598 (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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537A VAL* 6.2 1.6 - - + -
540A LEU* 3.7 37.0 - - + +
541A VAL* 4.6 20.6 - - + -
544A HIS* 4.1 37.7 - - + +
594A ASN 5.2 1.5 + - - +
595A THR* 2.9 13.6 + - - +
597A PRO* 1.3 77.4 - - - +
599A PHE* 1.3 63.2 + - + +
601A GLN* 2.8 32.6 + - + +
602A LEU* 3.2 19.2 + - + +
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Residues in contact with PHE 599 (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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540A LEU* 4.6 13.2 - - + -
574A THR* 4.1 20.9 - - + -
577A LEU* 3.9 26.2 - - + -
590A ILE* 4.3 12.1 - - + -
595A THR* 3.2 43.4 + - + -
596A ILE* 3.2 9.5 + - - +
598A LEU* 1.3 78.4 - - + +
600A VAL* 1.3 62.3 + - - +
602A LEU* 3.3 27.1 + - + +
603A LEU* 3.9 7.8 + - - +
614A ALA* 4.2 7.2 - - - +
617A VAL* 3.7 37.7 - - + -
618A LEU* 3.9 25.2 - - + +
621A LEU* 4.7 6.7 - - + -
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Residues in contact with VAL 600 (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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596A ILE* 3.0 35.3 + - + +
597A PRO* 3.7 6.7 - - + +
599A PHE* 1.3 76.5 - - - +
601A GLN* 1.3 62.3 + - + +
603A LEU* 3.2 29.2 + - + +
604A TYR* 3.9 12.8 - - + -
618A LEU* 4.7 9.6 - - + -
631A ILE* 4.7 4.0 - - + -
634A GLU* 4.2 20.0 - - + +
635A GLY 4.8 2.9 - - - +
636A ALA* 4.2 35.4 - - + +
639A PRO* 5.6 0.7 - - + -
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Residues in contact with GLN 601 (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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544A HIS* 4.7 17.4 + - + +
597A PRO 3.3 15.1 + - - +
598A LEU* 2.8 28.6 + - + +
600A VAL* 1.3 77.5 - - + +
602A LEU* 1.3 59.2 + - - +
603A LEU 3.1 5.4 - - - -
604A TYR* 3.3 30.9 + - + +
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Residues in contact with LEU 602 (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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540A LEU* 5.1 6.1 - - + -
544A HIS* 4.3 24.2 - - + +
570A VAL* 4.2 20.9 - - + -
574A THR* 3.8 31.2 - - + +
598A LEU* 3.2 20.3 + - + +
599A PHE* 3.5 20.9 - - + +
600A VAL 3.2 0.8 - - - -
601A GLN* 1.3 73.2 - - - +
603A LEU* 1.3 61.5 + - - +
604A TYR 3.0 7.0 + - - -
605A SER* 3.1 23.7 + - - +
610A ILE* 4.1 18.2 - - + +
611A GLN* 4.7 4.7 - - - +
614A ALA* 3.8 16.9 - - + +
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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