Contacts of the helix formed by residues 62 - 65 (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 LEU 62 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151 LEU* 2.7 26.6 + - + +
161 VAL 4.7 7.0 - - - +
171 VAL* 3.9 26.5 - - + -
611 THR* 1.3 73.2 - - - +
631 ASP* 1.3 63.4 + - - +
641 GLU 3.3 3.1 - - - -
651 MET* 3.0 35.0 + - + +
423 ASN* 2.9 30.2 + - - +
443 ILE* 4.2 26.7 - - + -
2193 PHE 4.1 11.0 - - - +
2203 CYS* 4.0 9.9 - - - -
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Residues in contact with ASP 63 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121 ASN* 3.2 35.7 + - + +
141 VAL* 3.0 38.2 + - - +
151 LEU* 2.8 26.4 + - - -
611 THR* 3.4 9.6 - - - +
621 LEU* 1.3 72.7 - - - +
641 GLU* 1.3 58.0 + - - +
661 SER* 2.9 32.1 + - - -
691 SER* 3.9 1.7 - - - -
434 LEU* 3.7 19.6 - - + +
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Residues in contact with GLU 64 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611 THR* 4.9 3.6 + - - +
621 LEU 3.3 1.0 - - - -
631 ASP* 1.3 77.9 - - - +
651 MET* 1.3 57.6 + - - +
661 SER 3.2 1.7 - - - +
691 SER* 2.7 32.5 + - - +
701 PHE* 4.5 2.3 + - - -
731 ARG* 3.9 15.8 + - - +
1063 PHE* 4.0 16.1 - - + -
2213 LEU 5.0 5.6 - - - +
2223 ARG* 3.7 13.5 - - - +
2233 MET* 2.8 28.2 + - - -
2243 ALA* 2.9 23.8 + - - +
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Residues in contact with MET 65 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621 LEU* 3.0 31.5 + - - +
641 GLU* 1.3 75.8 - - - +
661 SER* 1.3 63.8 + - - +
701 PHE* 5.4 0.2 - - - -
423 ASN* 3.3 13.2 - - - +
433 LEU* 2.8 41.5 + - + +
443 ILE* 3.8 32.8 - - + +
473 CYS* 4.1 8.3 - - - -
1023 ILE* 4.9 0.7 - - + -
1063 PHE* 4.1 18.2 - - + -
2193 PHE* 5.0 0.4 - - + -
2203 CYS* 4.4 1.3 - - - -
2213 LEU* 3.5 59.9 - - + +
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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
------------------------------------------------------------
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