Contacts of the strand formed by residues 162 - 167 (chain 3) 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 THR 162 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341 LEU* 3.4 10.7 - - - +
351 ASP* 2.9 41.3 + - + +
361 ALA 4.1 0.2 - - - -
371 ALA* 3.0 39.2 + - + +
431 ASN* 6.2 1.6 - - + -
1163 SER* 4.1 11.9 - - - +
1173 PHE 3.2 20.2 - - - +
1183 MET* 3.7 5.8 - - - +
1553 TRP* 4.5 2.5 - - - -
1603 GLN 4.3 0.5 - - - +
1613 SER* 1.3 86.3 + - - +
1633 VAL* 1.3 73.5 + - - +
1643 SER* 5.0 1.3 - - - +
2123 PHE* 5.1 0.4 - - + -
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Residues in contact with VAL 163 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331 VAL* 3.2 16.4 - - + +
341 LEU* 4.1 9.2 - - + -
1153 PHE 4.0 0.2 - - - +
1163 SER* 3.2 4.5 - - - -
1173 PHE* 2.9 36.4 + - + +
1313 LEU* 3.9 16.8 - - + -
1533 VAL* 4.2 19.3 - - + -
1553 TRP* 3.4 57.0 - - + -
1623 THR* 1.3 76.1 - - - +
1643 SER* 1.3 68.9 + - - +
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Residues in contact with SER 164 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331 VAL* 2.9 33.1 + - - +
431 ASN* 3.4 21.4 + - - +
451 ILE* 3.8 25.1 - - - -
501 THR* 4.7 1.2 - - - +
1143 ARG* 4.4 5.5 - - - +
1153 PHE 3.2 4.7 - - - -
1163 SER* 2.9 21.5 + - - -
1313 LEU* 5.9 0.2 - - - -
1533 VAL* 4.3 5.6 - - - +
1623 THR* 5.0 1.6 - - - +
1633 VAL* 1.3 82.3 - - - +
1653 LEU* 1.3 60.1 + - - +
1663 VAL* 4.3 1.2 + - - -
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Residues in contact with LEU 165 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133 LEU 3.9 0.3 - - - +
1143 ARG* 3.7 0.9 - - - -
1153 PHE* 2.7 42.2 + - + +
1173 PHE* 4.5 10.5 - - + -
1313 LEU* 3.9 38.1 - - + +
1323 ALA* 4.7 4.3 - - - -
1333 TYR* 4.9 2.7 - - + +
1513 THR* 4.8 9.4 - - + +
1523 HIS* 4.4 6.3 - - - -
1533 VAL* 3.7 27.8 - - + +
1643 SER* 1.3 74.3 - - - +
1663 VAL* 1.3 72.4 + - - +
1673 VAL* 3.9 5.5 + - + -
1893 ILE* 4.0 35.4 - - + -
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Residues in contact with VAL 166 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451 ILE* 4.1 22.7 - - + -
461 GLN 4.3 10.3 - - - -
471 PRO* 3.8 25.1 - - + -
501 THR* 3.6 34.3 + - + +
1123 SER* 4.1 2.9 - - - -
1133 LEU 3.3 9.6 - - - +
1143 ARG* 4.8 2.9 - - + -
1513 THR* 4.3 9.5 - - - +
1643 SER 4.3 0.6 + - - -
1653 LEU* 1.3 82.1 - - - +
1673 VAL* 1.3 69.8 + - - +
1683 PRO* 3.1 14.1 - - + +
2163 CYS* 4.0 19.1 - - - -
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Residues in contact with VAL 167 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873 VAL* 4.0 17.0 - - + -
1113 GLY 4.7 0.3 - - - +
1123 SER* 3.3 3.3 - - - -
1133 LEU* 2.7 37.0 + - + +
1153 PHE* 3.5 33.9 - - + -
1333 TYR* 3.6 43.5 - - + +
1653 LEU* 4.5 3.4 - - + -
1663 VAL* 1.3 73.7 - - - +
1683 PRO* 1.3 67.5 - - - +
1893 ILE* 3.6 16.8 - - + -
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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