Contacts of the helix formed by residues 428 - 432 (chain A) in PDB entry 2O1S
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 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A PRO* 5.0 1.1 - - - -
424A VAL* 4.5 1.6 - - - +
425A GLY 2.9 16.5 + - - -
426A ALA 3.0 1.2 - - - -
427A ASP* 1.3 78.8 - - - +
429A GLN* 1.3 74.5 + - - -
430A THR 3.3 0.2 - - - -
431A HIS* 2.9 15.9 + - - +
432A GLN* 3.3 23.3 + - - +
594A GLN* 4.0 12.8 - - - -
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Residues in contact with GLN 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A HIS* 3.7 31.3 + - - -
106A PRO* 5.7 0.6 - - - +
109A TRP* 3.9 27.0 - - + -
428A GLY* 1.3 76.8 - - - +
430A THR* 1.3 61.4 + - - +
431A HIS 3.2 1.6 + - - -
432A GLN* 3.7 13.7 + - - +
435A PHE* 6.2 0.3 - - - -
591A PHE* 3.5 38.5 - - + +
592A ILE 3.2 20.0 + - - +
593A PRO* 3.6 22.8 - - - +
594A GLN* 3.9 4.9 - - - +
409B ILE* 4.0 13.3 - - + +
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Residues in contact with THR 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 3.4 11.3 - - + -
109A TRP* 4.6 11.4 - - + -
119A SER 5.3 1.3 - - - -
120A VAL* 3.6 21.3 - - - +
121A GLY* 3.4 7.2 - - - -
122A HIS* 2.9 28.9 + - - -
394A THR* 3.2 2.2 + - - -
427A ASP 3.9 1.4 + - - -
428A GLY 3.3 0.2 - - - -
429A GLN* 1.3 74.8 - - - +
431A HIS* 1.3 80.7 + - - +
432A GLN 3.8 0.2 - - - -
405B HIS* 3.6 26.1 - - + +
409B ILE* 4.0 24.0 - - + +
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Residues in contact with HIS 431 (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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49A HIS* 6.4 0.2 - + - -
78A VAL* 6.2 0.7 - - + -
107A PHE* 3.5 26.4 - + - -
121A GLY* 3.3 24.9 + - - -
122A HIS* 4.7 0.7 - + - -
291A ALA* 4.0 17.9 - - + +
392A TYR* 6.0 0.8 - - - -
394A THR* 3.3 21.4 - - + +
395A PHE* 4.0 22.6 - + - -
420A ARG* 4.9 1.2 - - - +
424A VAL* 3.5 16.5 - - + +
427A ASP* 3.7 31.5 + - + +
428A GLY 2.9 5.4 + - - +
430A THR* 1.3 110.0 + - - +
432A GLN* 1.3 65.2 + - - +
433A GLY 3.5 1.9 + - - -
3001A TPP 4.4 7.0 - - - -
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Residues in contact with GLN 432 (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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394A THR* 3.5 12.9 + - - -
397A GLN* 4.1 6.8 + - - -
422A GLY 4.1 1.6 - - - +
423A ILE* 3.1 10.3 - - - +
424A VAL* 2.7 35.0 + - - +
425A GLY 4.4 5.9 + - - +
428A GLY* 3.3 25.1 - - - +
429A GLN* 3.7 12.2 + - - +
430A THR 3.8 0.4 - - - -
431A HIS* 1.3 78.0 - - - +
433A GLY* 1.3 57.7 + - - +
434A ALA* 3.0 24.3 + - + +
435A PHE* 5.0 3.6 - - + -
587A LEU* 6.1 0.2 - - + -
592A ILE* 2.9 51.1 + - + +
593A PRO 3.9 4.4 + - - -
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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