Contacts of the strand formed by residues 207 - 215 (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 ALA 207 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1192 GLN* 3.8 7.4 - - - +
713 THR* 3.4 2.8 - - - -
723 LEU* 2.8 33.9 + - - +
1193 PHE* 3.8 10.1 - - + -
1213 GLY* 3.5 29.6 - - - +
1973 PHE* 3.5 21.1 - - + -
2063 THR* 1.3 77.5 - - - +
2083 GLU* 1.3 67.4 + - - +
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Residues in contact with GLU 208 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192 GLN* 5.0 3.9 + - - +
2272 CYS* 3.6 35.7 - - + -
2282 GLN* 5.2 4.9 - - + +
2302 GLN* 4.8 12.1 + - - +
693 THR* 3.3 27.8 + - + -
703 VAL 3.4 4.4 - - - +
713 THR* 3.0 31.7 + - - +
723 LEU* 4.9 0.4 - - - -
1193 PHE* 4.2 3.1 - - - -
1203 CYS* 2.9 31.4 + - + +
1213 GLY 4.1 0.5 + - - -
2063 THR* 4.8 4.5 + - - -
2073 ALA* 1.3 79.7 - - - +
2093 MET* 1.3 63.9 + - - +
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Residues in contact with MET 209 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683 TYR 4.0 0.3 - - - +
693 THR* 3.5 7.2 - - - -
703 VAL* 3.0 60.2 + - + +
723 LEU* 3.9 21.8 - - + -
823 ILE* 4.6 5.8 - - + -
833 PHE* 3.7 29.2 - - + -
1173 PHE* 4.4 10.3 - - + -
1183 MET 3.3 13.9 - - - +
1193 PHE* 4.8 2.5 - - + -
1203 CYS* 4.8 0.4 - - - -
1293 VAL* 6.1 1.8 - - - -
1313 LEU* 6.2 0.4 - - - -
1553 TRP* 3.9 24.0 - - + -
1913 CYS* 4.9 7.2 - - - -
2083 GLU* 1.3 77.5 - - - +
2103 LEU* 1.3 74.3 + - - +
2113 CYS* 4.3 5.9 - - - -
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Residues in contact with LEU 210 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1212 THR* 4.5 0.2 - - + -
1892 PHE* 4.1 12.1 - - + -
2262 VAL* 4.0 27.6 - - + -
2272 CYS* 4.3 3.8 - - - -
523 LEU* 4.2 15.3 - - + -
683 TYR* 3.5 24.7 - - + +
693 THR* 3.6 19.5 - - + -
1173 PHE* 3.2 7.1 - - - +
1183 MET* 2.9 60.4 + - + +
1203 CYS* 4.3 12.8 - - - -
2093 MET* 1.3 74.1 - - - +
2113 CYS* 1.3 62.9 + - - +
2123 PHE* 3.8 13.6 - - + -
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Residues in contact with CYS 211 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523 LEU* 3.3 8.0 - - - +
533 ILE* 2.8 49.1 + - + +
553 ILE* 4.1 30.5 - - + -
683 TYR 4.5 4.8 + - - -
703 VAL* 4.3 3.1 - - - -
1163 SER 3.4 3.8 - - - -
1173 PHE* 3.6 30.3 - - + -
2093 MET* 4.3 16.4 - - - -
2103 LEU* 1.3 80.1 - - - +
2123 PHE* 1.3 63.1 + - - +
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Residues in contact with PHE 212 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371 ALA* 3.8 24.0 - - + -
1832 LEU* 3.7 28.5 - - + -
1892 PHE* 4.0 16.4 - + - -
503 ASP* 3.8 26.9 - - + +
513 THR 3.2 8.7 - - - +
523 LEU* 3.5 21.8 - - + -
533 ILE* 3.8 7.7 - - - +
1143 ARG 4.4 0.2 - - - -
1153 PHE* 3.4 5.7 - - - -
1163 SER* 2.8 50.5 + - - +
1173 PHE* 4.6 0.6 - - - -
1183 MET* 3.9 21.8 - - + -
1623 THR* 5.1 0.2 - - + -
2103 LEU* 3.8 22.9 - - + -
2113 CYS* 1.3 75.7 - - - +
2133 VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 213 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493 VAL 3.8 2.4 - - - +
503 ASP* 3.6 1.7 - - - -
513 THR* 3.2 22.5 + - - +
533 ILE* 3.9 18.4 - - + -
893 ILE* 5.1 5.4 - - + -
943 LEU* 4.3 7.2 - - + -
973 THR* 3.9 21.3 - - + +
993 ILE* 3.8 26.0 - - + +
1133 LEU* 4.9 5.2 - - + -
1143 ARG 3.3 10.1 - - - +
1153 PHE* 3.7 28.0 - - + -
2123 PHE* 1.3 77.5 - - - +
2143 SER* 1.3 72.1 + - - +
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Residues in contact with SER 214 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421 THR* 3.7 1.2 - - - +
473 CYS 3.7 11.4 - - - -
483 GLN 3.9 7.2 - - - -
493 VAL 3.8 15.3 - - - -
503 ASP* 2.8 24.1 + - - -
993 ILE* 3.9 11.4 - - - -
1133 LEU* 3.8 2.6 - - - +
1143 ARG* 2.8 54.8 + - - +
2133 VAL* 1.3 76.3 - - - +
2153 GLY* 1.3 59.5 + - - +
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Residues in contact with GLY 215 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473 CYS 2.8 18.8 + - - -
483 GLN* 4.0 14.0 - - - +
993 ILE* 3.5 12.2 - - - +
1123 SER 3.9 5.8 - - - -
1133 LEU* 4.7 0.9 - - - -
1143 ARG* 2.8 20.5 + - - -
2143 SER* 1.3 74.1 - - - +
2163 CYS* 1.3 66.8 + - - +
2193 PHE* 4.0 11.9 - - - -
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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
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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