Contacts of the helix formed by residues 590 - 595 (chain A) in PDB entry 4PJW
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 GLN 590 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A LEU* 3.7 23.6 - - + -
586A THR* 2.7 38.7 + - - +
587A ASN* 3.0 11.8 + - - +
589A LEU* 1.3 78.0 - - - +
591A LEU* 1.3 63.7 + - - +
592A PRO 3.7 0.2 - - - -
593A GLN* 3.5 35.6 + - - +
594A TYR* 3.2 24.0 - - + +
631A ALA* 4.2 11.4 - - - +
634A LYS* 5.9 1.9 - - - +
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Residues in contact with LEU 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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525A MSE 4.8 3.1 - - + -
526A LEU* 4.2 14.6 - - + -
529A ILE* 3.2 44.2 - - + -
563A ILE* 5.1 2.7 - - + -
567A PHE* 4.3 26.0 - - + -
571A LEU* 3.8 21.3 - - + -
588A LEU* 3.3 32.3 - - + +
590A GLN* 1.3 72.8 - - - +
592A PRO* 1.3 62.4 - - + +
593A GLN 2.9 4.3 - - - -
594A TYR* 2.7 39.7 + - - +
595A PHE* 4.0 11.2 + - + -
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Residues in contact with PRO 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LEU* 3.5 24.0 - - + -
588A LEU 4.0 0.9 - - - +
589A LEU* 3.5 12.6 - - + +
591A LEU* 1.3 93.0 - - + +
593A GLN* 1.3 56.1 + - + +
594A TYR 3.0 5.4 + - - -
595A PHE* 3.3 39.5 + - + +
597A LEU* 4.4 8.8 - - - +
612A LEU* 4.2 9.9 - - + -
635A THR* 3.9 23.8 - - + -
638A ALA* 4.7 7.2 - - + +
639A LEU* 4.4 15.9 - - + -
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Residues in contact with GLN 593 (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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560A ARG* 4.4 5.0 + - - -
589A LEU 4.4 4.3 + - - +
590A GLN* 3.5 37.4 + - - +
591A LEU 2.7 3.4 + - - -
592A PRO* 1.3 74.9 - - + +
594A TYR* 1.3 71.7 + - + +
595A PHE 3.6 1.2 - - - +
631A ALA* 4.8 1.2 + - - +
634A LYS* 3.8 37.0 + - - +
635A THR* 4.1 10.6 + - - +
638A ALA* 4.2 21.8 - - + -
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Residues in contact with TYR 594 (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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526A LEU* 4.1 15.2 - - + +
529A ILE* 3.9 22.0 - - + -
530A ARG* 3.1 49.2 + - + +
533A ALA* 3.5 28.4 - - + +
534A GLU* 4.1 14.2 + - - -
560A ARG* 3.1 31.1 + - - +
563A ILE* 4.9 5.6 - - + +
564A THR* 4.5 1.7 + - - -
590A GLN* 3.2 36.4 - - + +
591A LEU* 2.7 14.4 + - - +
593A GLN* 1.3 91.2 + - + +
595A PHE* 1.3 63.0 + - + +
596A ASP 3.8 0.3 + - - -
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Residues in contact with PHE 595 (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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560A ARG* 4.0 7.7 + - - -
563A ILE* 3.9 14.8 - - + -
564A THR* 3.4 29.8 - - + +
567A PHE* 3.8 39.3 - - + -
568A ALA* 4.1 6.3 - - - -
571A LEU* 4.6 4.5 - - + -
591A LEU* 4.0 16.4 - - + -
592A PRO* 3.3 41.0 + - + +
593A GLN 5.0 1.6 - - - +
594A TYR* 1.3 83.3 - - - +
596A ASP* 1.3 62.5 + - - +
597A LEU* 3.4 20.2 + - + +
600A TYR* 4.1 32.3 - + - -
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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