Contacts of the helix formed by residues 594 - 603 (chain A) in PDB entry 3HS0
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 ASN 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413A TYR* 3.5 7.2 - - - -
414A GLN* 3.9 15.3 - - + +
592A GLY 4.1 0.2 - - - -
593A GLN* 1.3 91.1 + - + +
595A ASN* 1.3 69.3 + - - +
596A LEU* 3.5 28.4 - - - +
597A GLY* 2.6 36.6 + - - -
598A VAL 3.4 7.6 + - - -
600A GLU* 5.1 2.5 + - - +
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Residues in contact with ASN 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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413A TYR* 3.3 26.7 + - - +
414A GLN 4.5 2.8 + - - -
416A GLN* 3.2 36.4 + - - +
509A ILE* 3.2 30.6 + - + +
511A ALA* 4.2 3.5 - - - +
594A ASN* 1.3 71.2 - - - +
596A LEU* 1.3 96.3 + - - +
598A VAL* 3.5 10.0 + - - +
599A PHE* 3.2 24.0 - - + -
606A LEU* 6.2 0.4 - - - -
612A LEU* 4.3 14.5 - - - +
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Residues in contact with LEU 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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594A ASN* 3.2 20.8 - - + +
595A ASN* 1.3 92.4 + - - +
597A GLY* 1.3 64.5 + - - +
599A PHE* 3.2 6.8 + - - +
600A GLU* 2.9 42.1 + - - +
606A LEU* 5.1 5.4 - - + -
612A LEU* 4.1 26.7 - - + +
613A ASN 3.1 37.9 - - - +
614A THR* 3.9 11.4 - - + +
615A LYS* 5.0 1.1 - - + +
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Residues in contact with GLY 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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592A GLY* 4.1 6.7 - - - -
593A GLN* 4.4 7.0 - - - -
594A ASN* 2.6 28.4 + - - -
596A LEU* 1.3 72.6 - - - +
598A VAL* 1.3 53.4 + - - +
600A GLU* 4.0 12.3 + - - -
601A ASP* 2.8 43.2 + - - +
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Residues in contact with VAL 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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413A TYR* 4.0 16.8 - - + -
499A VAL* 4.5 6.5 - - + -
511A ALA* 3.7 37.7 - - + +
512A ASP* 3.8 21.3 - - - +
513A SER* 3.9 10.2 + - - +
591A SER* 3.5 31.9 - - - +
592A GLY* 3.8 4.2 - - - +
594A ASN 3.4 3.5 + - - +
595A ASN 3.6 8.3 - - - +
596A LEU 3.2 0.4 - - - -
597A GLY* 1.3 75.5 - - - +
599A PHE* 1.3 67.6 + - + +
601A ASP* 3.7 2.4 - - - +
602A ALA* 3.0 21.8 + - - +
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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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6A ILE* 3.8 24.7 - - + -
460A LEU* 5.4 0.7 - - + -
499A VAL* 4.3 15.3 - - + -
501A TYR* 4.0 26.0 - + + -
509A ILE* 4.4 8.1 - - + -
511A ALA* 3.4 25.8 - - + -
595A ASN 3.2 21.1 - - - -
596A LEU* 3.2 6.5 + - - +
598A VAL* 1.3 76.6 - - - +
600A GLU* 1.3 68.0 + - - +
602A ALA* 3.0 15.6 + - - +
604A LEU* 3.0 47.2 + - + +
606A LEU* 3.8 33.4 - - + -
614A THR* 4.3 13.0 - - + -
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Residues in contact with GLU 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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585A PHE 5.1 0.5 - - - +
587A CYS* 5.3 2.8 - - - -
594A ASN* 5.1 2.2 + - - +
596A LEU* 2.9 36.7 + - - +
597A GLY* 3.7 11.1 - - - +
599A PHE* 1.3 71.9 - - - +
601A ASP* 1.3 65.4 + - - +
603A GLY* 3.2 13.7 + - - -
604A LEU 3.9 7.8 + - - +
614A THR* 3.6 21.4 - - - -
615A LYS* 3.1 62.4 + - + +
617A ARG* 4.5 12.1 + - - -
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Residues in contact with ASP 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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331A TYR* 4.3 8.5 + - - -
497A ARG* 4.2 3.3 + - - -
513A SER* 5.6 1.1 - - - +
586A GLY 3.9 0.3 - - - -
587A CYS* 3.1 31.0 + - - +
588A THR* 3.1 45.2 + - - +
591A SER 3.9 12.4 - - - +
592A GLY* 4.0 9.2 - - - -
597A GLY* 2.8 25.7 + - - +
598A VAL 3.7 3.8 - - - +
600A GLU* 1.3 78.4 - - - +
602A ALA* 1.3 56.5 + - - +
603A GLY 3.2 0.2 - - - -
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Residues in contact with ALA 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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462A LEU* 3.5 18.4 - - + +
497A ARG* 3.6 22.2 + - - +
499A VAL* 3.6 30.5 - - + -
513A SER* 4.4 7.0 - - - -
584A ASP* 5.5 0.2 - - - +
586A GLY* 3.6 12.3 + - - -
598A VAL 3.0 11.1 + - - +
599A PHE* 3.0 11.7 + - - +
601A ASP* 1.3 78.0 - - - +
603A GLY* 1.3 58.5 + - - +
604A LEU* 4.6 2.2 - - + +
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Residues in contact with GLY 603 (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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8A PRO* 3.8 4.5 - - - +
9A ALA* 2.9 27.9 + - - +
462A LEU* 5.0 1.0 - - - +
465A GLY 5.6 1.0 - - - +
585A PHE* 3.5 31.9 - - - +
586A GLY* 4.0 0.2 - - - -
599A PHE 3.2 1.4 + - - -
600A GLU 3.2 10.0 + - - -
601A ASP 3.2 1.2 - - - -
602A ALA* 1.3 81.5 - - - +
604A LEU* 1.3 61.8 + - - +
617A ARG* 5.4 0.2 - - - -
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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