Contacts of the helix formed by residues 178 - 185 (chain 2) 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 178 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2501 PRO* 4.5 2.5 - - - +
2511 PRO 4.7 1.8 + - - -
2531 ALA* 3.7 20.0 - - + +
2741 VAL* 4.8 4.9 - - + -
2751 ALA 6.3 0.2 - - - +
2761 ILE* 4.0 18.4 - - + -
1712 TRP* 3.7 35.2 - - + +
1722 LEU* 4.0 9.2 - - + -
1732 ASN* 2.9 9.4 - - - +
1772 THR* 1.3 72.6 - - - +
1792 LEU* 1.3 63.9 - - - +
1802 GLY 3.2 0.9 - - - +
1812 ASN* 3.1 29.9 + - - +
1822 LEU 4.1 0.2 + - - -
673 MET* 4.5 1.8 - - + -
683 TYR* 3.8 16.6 - - - +
963 THR* 3.7 37.7 - - + +
1013 GLU* 5.4 2.0 - - - +
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Residues in contact with LEU 179 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232 LEU* 4.2 16.7 - - + +
1702 ASN 3.8 11.9 - - - +
1712 TRP* 3.1 21.2 + - - +
1732 ASN* 3.1 20.7 + - - +
1782 LEU* 1.3 71.8 - - - +
1802 GLY* 1.3 63.6 + - - +
1812 ASN 3.0 1.6 + - - -
1822 LEU* 3.1 39.6 + - + +
1832 LEU* 4.8 0.7 - - - +
2242 ILE* 4.2 17.0 - - + -
2262 VAL* 4.5 12.3 - - + -
523 LEU* 5.1 2.6 - - + +
653 VAL* 3.9 30.3 - - + -
683 TYR* 4.0 24.1 + - + -
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Residues in contact with GLY 180 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1782 LEU* 3.2 0.8 + - - +
1792 LEU* 1.3 77.2 - - - +
1812 ASN* 1.3 62.5 + - - +
1822 LEU 3.4 1.5 + - - -
1832 LEU* 4.1 6.1 - - - +
513 THR* 3.3 6.6 - - - -
523 LEU* 2.9 39.6 + - - +
683 TYR* 3.0 35.1 + - - -
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Residues in contact with ASN 181 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2501 PRO* 3.4 25.5 - - + +
2511 PRO* 3.9 18.6 + - - +
1782 LEU* 3.1 16.3 + - - +
1792 LEU 3.0 1.6 + - - -
1802 GLY* 1.3 77.8 - - - +
1822 LEU* 1.3 63.6 + - - +
1832 LEU 3.0 3.7 + - - +
1842 ILE* 3.1 25.1 + - + +
513 THR* 3.4 15.6 - - + -
523 LEU 4.8 0.3 - - - +
963 THR 3.1 21.8 + - - -
973 THR* 3.6 4.7 - - - -
983 LEU* 3.0 32.3 + - + +
1013 GLU* 4.8 1.0 + - - +
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Residues in contact with LEU 182 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2501 PRO* 4.6 2.5 - - + -
1232 LEU* 4.2 11.4 - - + -
1252 VAL* 3.9 24.9 - - + +
1272 ILE* 3.9 26.7 - - + -
1732 ASN* 3.2 42.8 - - + +
1782 LEU 4.1 0.4 + - - -
1792 LEU* 3.1 25.8 + - + +
1802 GLY 3.4 0.2 - - - -
1812 ASN* 1.3 74.3 - - - +
1832 LEU* 1.3 56.9 + - - +
1842 ILE 2.9 5.4 - - - -
1852 PHE* 2.9 48.9 + - + +
2222 VAL* 4.9 14.8 - - + -
2242 ILE* 5.1 0.9 - - + -
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Residues in contact with LEU 183 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232 LEU* 4.2 28.0 - - + -
1802 GLY 4.1 11.4 - - - +
1812 ASN 3.0 0.6 - - - -
1822 LEU* 1.3 79.2 - - - +
1842 ILE* 1.3 57.6 + - - +
1852 PHE 3.0 2.9 - - - +
1872 HIS* 3.1 46.9 + - + +
1892 PHE* 4.4 4.5 - - + -
493 VAL* 3.7 12.1 - - - +
503 ASP* 3.2 28.9 - - + +
513 THR* 4.0 9.2 - - + -
523 LEU* 4.3 14.8 - - + -
2123 PHE* 3.7 33.9 - - + -
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Residues in contact with ILE 184 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2481 PRO* 3.9 45.4 - - + +
2491 ARG* 4.0 3.4 - - - +
2501 PRO* 3.9 24.0 - - + -
352 TYR* 4.9 6.6 + - - -
1812 ASN 3.1 19.1 + - - +
1822 LEU 2.9 1.6 + - - -
1832 LEU* 1.3 77.3 - - - +
1852 PHE* 1.3 64.2 + - + +
1862 PRO* 4.6 1.4 - - - +
463 MET* 4.4 8.5 - - + -
493 VAL* 4.1 27.6 - - + -
513 THR* 4.9 2.3 - - + +
983 LEU* 3.7 30.7 - - + -
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Residues in contact with PHE 185 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141 THR* 4.9 0.7 - - - -
2481 PRO 3.5 19.5 - - - -
2491 ARG* 3.4 34.5 - - + -
2501 PRO* 3.5 18.4 - - + -
352 TYR* 3.9 8.7 - - - -
1252 VAL* 3.6 6.3 - - + -
1262 MET 3.6 11.4 - - - +
1272 ILE* 3.7 24.2 - - + -
1282 PRO* 3.5 31.0 - - + -
1752 ASP* 6.2 0.4 - - - -
1822 LEU* 2.9 38.5 + - + +
1832 LEU 3.4 1.0 - - - +
1842 ILE* 1.3 83.3 - - + +
1862 PRO* 1.3 74.6 - - + +
1872 HIS* 2.9 21.5 + - - +
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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