Contacts of the helix formed by residues 57 - 63 (chain C) in PDB entry 1QGN
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 ASP 57 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C SER* 1.3 73.1 + - - +
58C GLY* 1.3 57.5 + - - +
60C VAL* 3.7 8.5 - - - +
61C ALA* 2.8 31.2 + - - +
126C LEU* 3.6 12.1 - - - +
242C PRO 4.0 0.2 - - - +
243C LEU* 3.5 35.7 - - + +
246C LYS* 2.8 36.0 + - - -
311C HIS* 6.0 0.2 - - + -
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Residues in contact with GLY 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ASP* 4.5 3.6 - - - -
56C SER* 2.9 9.3 + - - -
57C ASP* 1.3 79.8 - - - +
59C SER* 1.3 61.7 + - - +
60C VAL 3.2 0.5 + - - -
61C ALA* 3.4 2.6 + - - +
62C ILE* 3.3 27.5 + - - +
311C HIS* 3.4 41.1 + - - +
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B GLU* 3.3 17.8 - - - +
430B ASP* 2.9 25.3 + - - +
433B ASP* 2.6 31.4 + - - +
54C LEU* 3.6 24.4 - - - +
56C SER* 2.9 6.3 + - - -
58C GLY* 1.3 75.9 - - - +
60C VAL* 1.3 57.7 + - - +
62C ILE* 3.7 0.8 + - - -
63C HIS* 3.2 31.7 + - - +
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Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 5.2 9.0 - - + +
54C LEU* 4.2 28.3 - - + +
55C ASN 5.4 0.4 - - - -
56C SER 3.0 17.4 + - - +
57C ASP* 3.7 12.6 - - - +
59C SER* 1.3 76.6 - - - +
61C ALA* 1.3 63.5 + - - +
62C ILE 2.9 1.8 - - - -
64C ALA* 2.7 52.2 + - + +
125C ALA* 3.8 18.2 - - + -
126C LEU* 3.8 18.2 - - + +
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ASP 2.8 18.9 + - - +
58C GLY* 3.4 7.2 + - - +
60C VAL* 1.3 75.7 - - - +
62C ILE* 1.3 57.3 + - + +
122C LYS* 3.0 30.2 + - - +
126C LEU* 3.9 25.8 - - + +
243C LEU* 5.5 1.3 - - + -
307C MET* 3.6 27.0 - - + +
310C LEU* 4.5 11.9 - - + -
311C HIS* 5.3 3.6 - - + +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B CYS* 3.9 15.9 - - + +
393B GLU* 4.4 9.9 - - + -
428B VAL* 3.6 24.0 - - + -
429B GLU* 4.0 14.1 - - + +
58C GLY 3.3 17.4 + - - +
59C SER 3.8 1.6 - - - +
60C VAL 2.9 2.0 - - - -
61C ALA* 1.3 79.8 - - - +
63C HIS* 1.3 86.1 + - + +
66C GLU* 3.4 1.6 - - - +
122C LYS* 2.9 20.6 + - - +
307C MET 4.8 0.2 - - - +
308C LYS* 3.1 59.3 + - + +
311C HIS* 4.1 2.5 - - + -
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Residues in contact with HIS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B ILE* 3.8 18.4 + - + +
384B TYR* 4.3 9.1 - + - -
393B GLU* 4.1 17.8 - - + +
394B SER 4.7 0.4 + - - -
429B GLU* 3.0 40.6 + - + +
50C TYR* 3.6 5.4 - - - -
54C LEU* 3.8 14.5 - - + +
59C SER 3.2 16.6 + - - +
62C ILE* 1.3 91.9 - - + +
64C ALA* 1.3 68.5 + - - +
65C GLY 3.2 0.5 + - - -
66C GLU* 3.0 17.6 + - + -
67C ARG* 3.0 52.2 + - + +
308C LYS* 6.0 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