Contacts of the helix formed by residues 595 - 600 (chain A) in PDB entry 4UH6
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 GLY 595 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A TYR 4.0 0.8 - - - -
594A MET* 1.3 72.6 - - - +
596A THR* 1.3 57.2 + - - +
598A ILE* 3.1 7.6 + - - +
599A GLY* 2.8 25.1 + - - -
639A ASN* 3.7 4.9 - - - +
642A VAL* 4.0 7.5 - - - +
643A LEU* 4.3 13.9 - - - -
653A ILE* 4.0 21.2 - - - +
654A VAL 2.9 14.4 + - - -
655A ASP* 4.7 1.5 - - - +
656A HIS* 6.2 0.2 - - - -
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Residues in contact with THR 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A MET* 3.2 29.3 - - - +
595A GLY* 1.3 72.7 - - - +
597A GLU* 1.3 65.3 + - - +
598A ILE 3.2 0.2 - - - -
600A VAL* 2.9 38.5 + - + +
601A ARG* 3.2 9.4 + - - +
639A ASN* 3.5 12.6 - - - +
656A HIS* 3.4 35.6 + - + +
686A PRO* 4.9 0.2 - - + -
687A PRO* 3.7 17.7 - - + +
688A MET* 3.9 12.1 - - + -
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Residues in contact with GLU 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A TYR* 3.4 15.9 - - + -
594A MET* 2.9 31.4 + - + +
596A THR* 1.3 79.1 - - - +
598A ILE* 1.3 58.6 + - - +
601A ARG* 3.3 10.1 - - + +
602A ASP* 2.9 31.6 + - - +
687A PRO* 5.9 0.2 - - - -
750A HEM 3.4 33.3 - - + +
800A Q1T 2.6 74.0 + - - +
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Residues in contact with ILE 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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551A ILE* 5.6 0.7 - - + -
566A TRP* 3.4 47.1 - - + +
593A TYR* 3.6 28.7 - - + -
594A MET 5.4 0.2 - - - +
595A GLY 3.1 5.0 + - - +
597A GLU* 1.3 78.0 - - - +
599A GLY* 1.3 61.4 + - - +
600A VAL 3.4 0.2 + - - -
602A ASP* 3.4 10.3 + - + +
603A TYR* 3.0 54.6 + - + +
642A VAL* 4.3 12.6 - - + -
646A PHE* 3.6 31.2 - - + -
653A ILE* 4.8 1.6 - - + -
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Residues in contact with GLY 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A GLY 2.8 15.5 + - - -
598A ILE* 1.3 74.7 - - - +
600A VAL* 1.3 57.3 + - - +
603A TYR* 3.8 1.7 - - - +
604A CYS* 3.4 21.3 - - - -
638A ILE* 3.5 11.1 - - - +
639A ASN* 3.2 29.9 + - - -
642A VAL* 3.9 17.0 - - - +
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Residues in contact with VAL 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A THR* 2.9 24.6 + - + +
599A GLY* 1.3 78.3 - - - +
601A ARG* 1.3 59.7 + - - +
604A CYS* 3.0 29.8 + - - +
605A ASP* 3.4 4.3 + - - +
635A LEU* 3.9 18.2 - - + -
639A ASN* 3.4 25.6 - - - +
687A PRO* 3.7 18.8 - - + +
688A MET* 3.7 21.3 - - + -
691B SER* 3.0 27.4 - - - +
692B ILE* 4.9 3.1 - - + +
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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