Contacts of the helix formed by residues 66 - 72 (chain 1) in PDB entry 1QJX
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 SER 66 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151 LEU* 5.0 1.6 - - - -
631 ASP 2.9 19.9 + - - -
641 GLU 3.2 0.4 - - - -
651 MET* 1.3 82.1 - - - +
671 VAL* 1.3 59.6 + - - +
681 GLU* 4.1 1.7 - - - +
691 SER* 3.0 18.4 + - - -
701 PHE* 2.8 27.1 + - - +
413 LYS 3.7 7.2 - - - -
423 ASN* 3.5 14.9 - - - +
434 LEU* 3.6 31.2 - - - +
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Residues in contact with VAL 67 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651 MET 3.8 0.6 + - - -
661 SER* 1.3 72.3 - - - +
681 GLU* 1.3 63.9 + - - +
701 PHE* 3.8 6.5 - - - +
711 LEU* 3.1 34.3 + - + +
1131 PHE* 4.4 16.2 - - + -
2431 THR* 3.8 32.9 - - + +
2451 ALA* 4.3 13.2 - - + +
403 VAL* 3.6 32.3 - - + +
413 LYS* 3.1 20.5 + - - +
423 ASN* 4.2 3.8 - - - +
433 LEU* 5.1 2.9 - - + +
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Residues in contact with GLU 68 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661 SER* 3.1 7.0 - - - +
671 VAL* 1.3 80.1 - - - +
691 SER* 1.3 59.0 + - - +
721 GLY* 2.9 29.3 + - - -
2401 ALA 4.5 1.8 - - - +
2411 LYS* 3.8 4.7 - - - -
2421 HIS* 2.9 22.9 + - - -
2431 THR* 2.8 37.8 + - - +
404 ALA* 3.4 16.1 - - + +
414 SER* 3.0 39.7 + - - +
434 LEU* 4.2 13.0 - - + -
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Residues in contact with SER 69 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631 ASP 3.9 2.9 - - - -
641 GLU* 2.7 31.5 + - - -
661 SER* 3.0 20.2 + - - -
681 GLU* 1.3 76.9 - - - +
701 PHE* 1.3 67.4 + - - +
721 GLY* 3.3 8.1 + - - -
731 ARG* 3.0 42.1 + - - +
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Residues in contact with PHE 70 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641 GLU 4.5 2.4 + - - +
651 MET 5.4 0.7 - - - -
661 SER 2.8 19.6 + - - +
671 VAL* 3.3 7.2 + - - +
691 SER* 1.3 76.2 + - - +
711 LEU* 1.3 75.5 + - + +
731 ARG* 4.5 2.9 - - - +
1091 LYS* 2.8 79.7 + - + -
1121 MET* 4.1 15.3 - - + -
1131 PHE* 4.4 9.6 - + - -
433 LEU* 3.5 40.8 - - + -
1023 ILE* 6.2 0.9 - - + -
1053 TYR* 3.9 33.9 - + + -
1063 PHE* 4.8 7.9 - + - -
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Residues in contact with LEU 71 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671 VAL* 3.1 21.1 + - + +
681 GLU 3.9 0.2 - - - -
701 PHE* 1.3 97.1 - - + +
721 GLY* 1.3 56.4 + - - +
731 ARG 3.1 14.9 + - - +
1091 LYS* 3.9 33.4 - - + +
1101 PHE* 4.1 32.6 - - + +
1131 PHE* 4.4 14.4 - - + -
1161 ALA* 5.5 3.1 - - + -
2401 ALA* 3.5 30.3 + - + +
2431 THR* 3.9 24.9 - - + +
2451 ALA* 5.3 2.5 - - + -
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Residues in contact with GLY 72 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681 GLU* 2.9 22.0 + - - -
691 SER* 3.3 5.5 + - - -
711 LEU* 1.3 76.9 - - - +
731 ARG* 1.3 63.1 + - - +
2391 LYS* 3.4 20.6 + - - +
2401 ALA 3.5 16.2 - - - -
153 THR 4.9 0.7 - - - +
163 THR* 5.4 3.1 - - - -
173 ASP 5.5 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