Contacts of the helix formed by residues 590 - 603 (chain A) in PDB entry 3N00
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 LEU 590 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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586A THR* 3.0 30.9 + - + +
587A LYS* 3.4 19.5 - - + +
588A LEU 3.1 0.8 - - - -
589A LEU* 1.3 74.6 - - + +
591A LYS* 1.3 67.6 + - - +
592A LEU 3.1 2.2 - - - -
593A PRO* 3.2 21.1 - - + +
594A ASP* 3.3 17.1 - - - +
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Residues in contact with LYS 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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523A PHE* 4.1 24.5 - - + -
526A LYS* 4.2 34.6 - - + +
527A LEU* 4.5 12.3 - - + +
530A LEU* 4.0 18.1 - - + +
540A PHE* 3.7 20.4 - - + -
587A LYS* 2.9 31.6 + - - +
588A LEU* 3.0 19.9 + - - +
590A LEU* 1.3 84.5 - - - +
592A LEU* 1.3 59.3 + - - +
594A ASP* 3.4 12.2 + - - +
595A LEU* 3.0 31.3 + - - +
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Residues in contact with LEU 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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478A GLU* 4.9 3.6 - - - +
540A PHE* 4.3 10.3 - - + -
543A VAL* 4.8 6.5 - - + -
544A VAL* 4.0 35.0 - - + -
547A SER* 4.3 23.8 - - - +
563A GLN* 5.4 2.2 - - - +
567A LEU* 5.6 1.1 - - + -
588A LEU 4.6 0.2 - - - +
589A LEU* 3.5 34.1 - - + +
591A LYS* 1.3 74.9 - - - +
593A PRO* 1.4 73.3 - - + +
595A LEU* 3.2 7.5 + - + +
596A ARG* 3.0 30.2 + - - +
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Residues in contact with PRO 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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589A LEU 3.6 4.7 - - - +
590A LEU* 3.2 27.1 - - + +
592A LEU* 1.4 95.4 - - + +
594A ASP* 1.3 57.6 + - - +
596A ARG* 3.2 10.3 + - + +
597A THR* 2.9 31.5 + - - -
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Residues in contact with ASP 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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523A PHE* 4.1 15.2 - - + -
526A LYS* 3.5 30.3 + - - +
590A LEU* 3.3 19.1 - - - +
591A LYS* 3.4 19.6 + - - +
592A LEU 3.2 0.2 - - - -
593A PRO* 1.3 79.3 - - - +
595A LEU* 1.3 57.1 + - - +
597A THR* 3.1 8.2 + - - +
598A LEU* 2.9 34.2 + - + +
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Residues in contact with LEU 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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477A PHE* 5.5 0.2 - - - -
478A GLU* 3.5 25.8 - - + +
481A MET* 3.5 35.0 - - + -
482A VAL* 4.0 8.7 - - + -
523A PHE* 3.6 25.4 - - + -
540A PHE* 4.3 4.9 - - + -
544A VAL* 3.7 37.7 - - + -
591A LYS 3.0 22.5 + - - +
592A LEU* 3.6 8.5 - - + +
594A ASP* 1.3 73.1 - - - +
596A ARG* 1.3 61.0 + - - +
598A LEU* 3.9 5.9 - - + +
599A ASN* 2.9 30.3 + - - +
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Residues in contact with ARG 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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478A GLU* 3.7 21.6 + - - +
547A SER* 2.8 28.5 + - - -
548A ALA* 4.2 2.0 + - - +
549A ASP* 3.7 39.6 + - - +
592A LEU* 3.0 19.5 + - - +
593A PRO* 3.2 12.8 + - + +
595A LEU* 1.3 77.4 - - - +
597A THR* 1.3 56.4 + - - +
599A ASN* 3.4 5.4 - - - +
600A ASN* 2.8 51.4 + - - +
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Residues in contact with THR 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 PRO 2.9 14.7 + - - -
594A ASP* 3.5 9.9 - - - -
596A ARG* 1.3 74.4 - - - +
598A LEU* 1.3 68.3 + - + +
600A ASN* 3.1 6.9 + - - +
601A MET* 3.0 46.0 + - + +
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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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477A PHE* 3.7 2.6 - - - -
481A MET* 4.3 21.5 - - + -
519A ALA* 3.6 37.9 - - + +
520A MET* 4.8 2.0 - - + +
523A PHE* 3.7 39.9 - - + -
594A ASP* 2.9 21.8 + - + +
595A LEU* 3.9 16.8 - - + +
597A THR* 1.3 73.9 - - + +
599A ASN* 1.3 64.1 + - - +
601A MET* 4.8 1.6 - - - -
602A HIS* 2.9 41.0 + - + +
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Residues in contact with ASN 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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474A ALA 3.9 12.9 + - - -
477A PHE* 3.6 23.3 - - + +
478A GLU* 2.9 31.7 + - + +
595A LEU 2.9 18.6 + - - +
596A ARG* 3.4 6.0 + - - +
598A LEU* 1.3 76.4 - - - +
600A ASN* 1.3 69.1 + - - +
601A MET 3.1 0.9 + - - -
603A SER* 2.8 50.8 + - - -
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Residues in contact with ASN 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 ARG* 2.8 43.9 + - - +
597A THR* 3.1 7.0 + - - +
599A ASN* 1.3 84.3 + - - +
601A MET* 1.3 60.6 + - + +
603A SER* 4.8 2.4 + - - -
604A GLU* 5.9 1.7 + - - +
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Residues in contact with MET 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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597A THR* 3.0 34.8 + - + +
598A LEU* 3.9 3.1 - - - +
600A ASN* 1.3 83.7 - - + +
602A HIS* 1.3 83.3 + - + +
603A SER 3.8 0.2 - - - -
604A GLU* 4.9 7.2 + - - +
605A LYS* 5.2 4.0 + - - +
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Residues in contact with HIS 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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477A PHE* 3.7 10.2 - - + -
515A ASP* 3.5 35.0 - - + -
516A LEU* 3.3 31.4 - - + -
519A ALA* 3.5 23.6 - - + +
598A LEU* 2.9 33.8 + - + +
601A MET* 1.3 98.8 + - + +
603A SER* 1.3 58.7 + - - +
604A GLU 3.0 6.5 - - - -
605A LYS* 2.9 44.9 + - + +
2051B LEU* 4.3 1.6 - - - +
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Residues in contact with SER 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A PHE* 3.9 22.9 - - - -
599A ASN* 2.8 38.7 + - - -
600A ASN* 4.8 3.6 + - - -
602A HIS* 1.3 75.2 - - - +
604A GLU* 1.3 68.3 + - - +
605A LYS 3.3 0.4 - - - -
2051B LEU* 3.5 3.2 + - - +
2052B ALA* 2.7 46.2 + - - +
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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