Contacts of the helix formed by residues 589 - 599 (chain A) in PDB entry 3PE3
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 589 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557A ASN* 3.4 29.9 + - + +
586A ASP* 4.4 0.2 + - - -
587A ASP* 2.8 35.7 + - - +
588A GLY* 1.3 79.6 - - - +
590A ASN* 1.3 64.8 + - - +
591A PHE* 3.6 10.6 - - - -
592A ARG* 3.3 9.4 + - - +
593A VAL* 3.2 21.4 + - - +
806A LYS* 4.5 1.1 - - - +
811A GLU* 3.3 23.8 - - - +
314B PRO* 6.3 3.1 - - + -
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Residues in contact with ASN 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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565A GLN* 5.0 0.4 - - - -
588A GLY 5.0 0.7 - - - +
589A THR* 1.3 71.1 - - - +
591A PHE* 1.3 56.4 + - + +
593A VAL* 2.9 15.5 + - + +
594A LYS* 2.7 37.1 + - - +
806A LYS* 4.2 12.6 + - - +
811A GLU* 2.8 56.8 + - + +
812A GLU* 3.9 15.0 + - - +
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Residues in contact with PHE 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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556A GLY* 3.4 19.1 - - - +
557A ASN* 3.6 36.8 - - + -
561A SER* 4.0 8.7 - - - -
562A HIS* 3.4 29.8 - + - -
565A GLN* 3.2 30.7 - - - +
589A THR* 3.2 8.9 - - - -
590A ASN* 1.3 80.5 - - - +
592A ARG* 1.3 61.1 + - - +
594A LYS* 3.3 1.9 + - - +
595A VAL* 3.2 28.7 + - - +
701A MET* 3.6 18.8 - - + -
809A THR 3.8 16.2 - - - -
810A GLY 4.0 6.3 - - - -
811A GLU* 3.4 25.8 - - + -
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Residues in contact with ARG 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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555A PHE* 3.1 33.5 + - - +
556A GLY* 4.0 1.0 - - - -
582A ALA* 3.5 16.7 - - - +
584A SER* 2.9 34.4 + - - -
585A PRO 3.6 10.1 + - - -
586A ASP* 3.5 44.1 - - - +
587A ASP* 3.9 13.9 - - - +
589A THR* 3.3 9.8 + - - +
590A ASN 3.3 0.2 - - - -
591A PHE* 1.3 80.3 - - - +
593A VAL* 1.3 59.8 + - + +
595A VAL* 4.2 2.8 - - - +
596A MET* 3.0 42.1 + - - +
602A PHE* 3.3 32.9 - - - -
604A ASP* 3.8 14.8 + - - +
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Residues in contact with VAL 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ASP* 5.7 3.8 - - - +
588A GLY* 4.8 7.0 - - - +
589A THR 3.2 16.8 + - - +
590A ASN* 2.9 22.1 + - + +
592A ARG* 1.3 78.1 - - + +
594A LYS* 1.3 64.5 + - - +
596A MET* 3.6 7.1 + - - +
597A ALA* 3.2 25.0 + - + +
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Residues in contact with LYS 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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565A GLN* 3.7 37.0 - - - +
566A SER* 3.5 25.8 + - - +
590A ASN 2.7 18.2 + - - +
591A PHE 3.3 4.5 + - - +
593A VAL* 1.3 72.7 - - - +
595A VAL* 1.3 64.9 + - + +
597A ALA* 3.1 4.4 + - - -
598A GLU* 2.8 65.9 + - - +
700A ASN* 4.2 13.1 + - - +
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Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A PHE* 4.0 26.2 - - + -
561A SER* 5.0 3.8 - - - +
564A MET* 5.6 0.9 - - + -
565A GLN* 4.2 32.5 - - + +
568A PRO* 4.3 9.9 - - + -
580A CYS* 3.6 28.3 - - - -
591A PHE 3.2 17.5 + - - +
592A ARG 4.5 2.0 - - - +
594A LYS* 1.3 75.9 - - - +
596A MET* 1.3 57.8 + - - +
598A GLU* 4.6 1.6 - - - +
599A ALA* 3.0 29.7 + - - +
602A PHE* 3.8 16.6 - - + -
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Residues in contact with MET 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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586A ASP* 4.3 12.8 - - - +
592A ARG* 3.0 45.7 + - - +
593A VAL* 3.9 6.5 - - - +
594A LYS 3.2 0.8 - - - -
595A VAL* 1.3 76.8 - - - +
597A ALA* 1.3 59.9 - - - +
598A GLU 3.7 0.2 + - - -
599A ALA 4.0 8.3 - - - +
602A PHE* 3.5 50.3 - - + +
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Residues in contact with ALA 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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593A VAL* 3.2 21.4 + - + +
594A LYS* 3.1 6.4 + - - +
596A MET* 1.3 79.8 - - - +
598A GLU* 1.3 64.7 + - + +
599A ALA 4.4 2.4 - - - +
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Residues in contact with GLU 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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565A GLN 4.2 4.0 - - - +
566A SER* 4.5 2.9 - - - +
568A PRO* 3.9 13.1 - - + +
569A GLY* 3.8 30.6 + - - +
594A LYS* 2.8 59.9 + - - +
595A VAL* 4.7 1.6 - - - +
597A ALA* 1.3 84.6 - - + +
599A ALA* 1.3 66.6 + - - +
600A ASN* 3.5 6.1 + - - -
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Residues in contact with ALA 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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568A PRO* 4.3 11.0 - - + +
578A VAL* 4.1 8.7 - - + +
580A CYS* 3.7 25.1 - - + -
595A VAL 3.0 19.5 + - - +
596A MET 4.0 9.9 - - - +
597A ALA 4.4 2.3 - - - +
598A GLU* 1.3 79.8 + - - +
600A ASN* 1.3 64.5 + - - +
601A HIS* 3.3 20.8 + - - +
602A PHE* 4.8 2.9 - - + +
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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