Contacts of the helix formed by residues 450 - 457 (chain A) in PDB entry 1KQG
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 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A SER 2.9 20.3 + - - +
169A ALA 3.0 24.1 + - - +
170A SER* 3.5 0.6 - - - +
171A ASN* 2.9 32.1 + - - +
449A SER* 1.3 80.6 + - - +
451A ILE* 1.3 64.0 + - - +
452A GLN 3.2 2.5 - - - +
453A GLY* 3.2 13.0 + - - -
454A LEU* 3.0 24.6 + - - +
626A ILE* 3.7 17.0 - - + -
627A ALA 2.9 22.3 + - - -
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Residues in contact with ILE 451 (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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167A SER* 3.5 18.5 + - - +
191A ASN* 3.5 15.5 - - - +
192A GLN* 3.9 10.5 - - + +
193A ALA* 3.5 30.3 - - + +
197A HIS* 4.8 15.7 - - + +
446A ARG* 3.8 14.8 - - + -
447A GLY* 3.8 22.7 - - - +
448A HIS* 3.1 21.3 + - + +
450A ASN* 1.3 77.5 - - - +
452A GLN* 1.3 60.5 + - - +
454A LEU 3.3 0.9 + - - +
455A THR* 2.8 39.8 + - - +
1017A MGD 5.5 4.9 - - - -
1018A MGD 6.4 1.8 - - - -
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Residues in contact with GLN 452 (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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54A SER* 6.4 0.2 - - - -
212A ALA* 4.2 13.8 - - - +
446A ARG* 3.4 40.9 + - + +
448A HIS 4.7 0.4 + - - -
450A ASN* 3.2 1.0 - - - +
451A ILE* 1.3 82.3 - - - +
453A GLY* 1.3 56.3 + - - +
455A THR* 3.5 6.0 + - - +
456A ASP* 2.9 64.0 + - - +
467A TYR* 3.5 9.7 + - - -
627A ALA* 3.5 20.4 + - + +
628A ASN 3.7 17.0 - - - +
629A SER 4.6 5.6 - - - +
631A ARG* 4.7 4.9 - - - -
771A TRP* 3.8 17.1 - - - +
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Residues in contact with GLY 453 (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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171A ASN* 3.3 15.3 - - - -
450A ASN* 3.2 23.4 + - - -
452A GLN* 1.3 75.9 - - - +
454A LEU* 1.3 59.8 + - - +
456A ASP* 3.2 1.8 + - - +
457A LEU* 2.8 33.7 + - - +
627A ALA* 3.8 4.3 - - - +
739A TYR* 3.5 14.4 - - - -
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Residues in contact with LEU 454 (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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165A CYS* 3.9 15.3 - - + -
166A ALA 3.4 37.0 - - - +
167A SER* 3.7 3.4 - - - +
169A ALA 4.0 3.1 - - - +
170A SER 4.4 6.7 - - - +
171A ASN* 4.7 1.3 - - - +
174A GLY* 4.5 12.8 - - - -
191A ASN* 3.8 35.2 - - + +
450A ASN* 3.0 38.0 + - - +
453A GLY* 1.3 74.0 - - - +
455A THR* 1.3 65.0 + - - +
457A LEU* 3.6 5.0 + - + +
458A GLY 3.3 3.8 + - - -
459A LEU* 3.0 39.5 + - + +
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Residues in contact with THR 455 (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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191A ASN* 4.4 4.1 + - - -
193A ALA* 3.9 20.1 - - + +
201A VAL* 4.5 17.7 - - + -
446A ARG* 6.0 1.8 - - - +
451A ILE* 2.8 21.2 + - - +
452A GLN* 3.7 8.7 - - - +
454A LEU* 1.3 76.5 - - - +
456A ASP* 1.3 63.5 + - - +
458A GLY* 3.0 14.2 + - - -
460A LEU* 4.5 18.2 - - + +
467A TYR* 3.3 33.4 + - + +
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Residues in contact with ASP 456 (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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452A GLN* 2.9 37.9 + - - +
453A GLY* 3.2 2.2 + - - +
455A THR* 1.3 77.7 - - - +
457A LEU* 1.3 57.8 + - - +
458A GLY 3.3 0.5 + - - -
466A GLY* 2.9 28.2 + - - -
467A TYR* 2.6 37.7 + - - -
627A ALA* 4.3 1.4 - - - +
736A CYS* 3.7 3.6 - - - -
738A ILE* 4.0 6.7 - - + -
739A TYR* 2.6 35.0 + - + +
771A TRP* 3.0 27.7 + - - -
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Residues in contact with LEU 457 (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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171A ASN* 3.1 52.5 - - + +
174A GLY* 4.4 3.8 - - - -
175A MET* 3.6 33.7 - - + +
178A GLN* 2.8 21.3 + - - +
453A GLY 2.8 18.4 + - - +
454A LEU* 3.6 1.1 + - - -
455A THR 3.3 0.4 - - - -
456A ASP* 1.3 71.4 - - - +
458A GLY* 1.3 56.0 + - - +
459A LEU* 3.6 17.4 - - + +
465A PRO* 3.4 16.3 - - + +
697A ASN* 4.3 5.6 - - - +
736A CYS* 3.7 26.2 - - + -
739A TYR* 4.0 10.3 - - + -
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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