Contacts of the helix formed by residues 595 - 600 (chain A) in PDB entry 2HX4
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 VAL 595 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591A THR* 2.8 27.6 + - - +
594A GLY* 1.3 74.3 - - - +
596A ARG* 1.3 59.5 + - - +
599A CYS* 3.1 25.7 + - - +
600A ASP* 3.4 5.4 + - - +
630A LEU* 4.0 17.0 - - + -
634A ASN* 3.3 25.3 + - - +
682A PRO* 3.7 20.0 - - + +
683A MET* 3.5 24.0 - - + -
686B SER* 2.9 27.1 + - - +
687B ILE* 5.0 3.0 - - + +
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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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591A THR 3.2 5.0 + - - +
592A GLU* 3.3 15.3 - - - +
595A VAL* 1.3 76.9 - - - +
597A ASP* 1.3 69.1 + - - +
600A ASP* 2.8 67.8 + - - +
603A ARG* 3.6 6.6 - - - +
682A PRO* 3.8 22.0 - - + +
750A HEM 4.6 5.2 + - - +
760A H4B 3.2 42.2 + - - -
799A 4HX 6.0 1.8 - - - +
686B SER* 3.6 20.3 - - - -
691B PHE* 3.7 16.1 - - - -
692B HIS* 3.9 12.9 + - - -
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Residues in contact with ASP 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLN* 5.9 0.3 + - - -
481A ARG* 5.2 0.2 + - - -
561A TRP* 3.4 43.6 + - + -
588A TYR* 4.5 5.9 + - - -
592A GLU 2.9 19.3 + - - +
593A ILE* 3.3 18.0 + - - +
596A ARG* 1.3 76.8 - - - +
598A TYR* 1.3 58.4 + - + +
603A ARG* 2.8 39.6 + - - +
604A TYR* 3.1 32.6 + - - +
799A 4HX 4.6 12.2 + - - +
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Residues in contact with TYR 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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517A PHE* 4.6 4.5 - + - -
546A ILE* 3.1 32.2 - - + +
559A LEU* 4.3 23.3 - - + -
560A LYS 3.2 18.9 + - - -
561A TRP* 3.6 26.6 + + - +
593A ILE* 2.8 28.8 + - + +
594A GLY* 3.7 9.2 - - - +
597A ASP* 1.3 79.7 - - - +
599A CYS* 1.3 59.8 + - - +
600A ASP 3.7 0.2 - - - -
604A TYR* 3.7 11.3 - - + -
605A ASN 3.2 7.3 + - - -
606A ILE* 2.9 48.8 + - + +
633A ILE* 4.0 18.4 - - + -
637A VAL* 3.8 22.7 - - + -
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Residues in contact with CYS 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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594A GLY 3.5 13.5 - - - -
595A VAL 3.1 16.2 + - - +
598A TYR* 1.3 79.3 - - - +
600A ASP* 1.3 68.5 + - - +
601A ASN* 3.3 5.2 + - - +
605A ASN* 4.4 5.4 + - - -
606A ILE* 4.3 4.0 - - - +
607A LEU* 3.5 38.7 - - + +
630A LEU* 3.7 14.6 - - + -
633A ILE* 3.4 33.2 - - - -
687B ILE* 4.3 9.5 - - + +
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Residues in contact with ASP 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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595A VAL 3.4 3.8 + - - +
596A ARG* 2.8 71.6 + - - +
598A TYR 3.7 0.2 - - - -
599A CYS* 1.3 77.7 - - - +
601A ASN* 1.3 66.0 + - - +
602A SER* 4.3 7.0 + - - +
603A ARG* 3.0 32.6 + - + +
605A ASN* 3.3 12.5 + - - -
686B SER* 4.2 7.8 + - - +
692B HIS* 3.5 20.0 + - - -
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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