Contacts of the strand formed by residues 75 - 83 (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 GLY 75 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731 ARG 3.3 3.2 + - - -
741 SER* 1.3 73.7 - - - +
761 CYS* 1.3 66.4 + - - -
771 ILE* 3.5 3.3 + - - +
1061 ILE* 3.8 19.9 - - - +
2371 TYR* 3.2 6.5 - - - -
2381 HIS 2.8 32.1 + - - +
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Residues in contact with CYS 76 (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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751 GLY* 1.3 72.4 - - - -
771 ILE* 1.3 65.6 + - - +
781 HIS 3.6 20.2 - - - -
791 GLU* 4.0 11.9 - - - -
1031 MET* 3.2 38.5 - - + +
1051 GLN* 6.2 0.2 - - - +
1061 ILE* 4.5 5.4 - - - +
2351 ARG* 4.3 5.8 - - - -
2361 ILE 3.5 8.5 - - - -
2371 TYR* 3.3 30.2 - - + +
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Residues in contact with ILE 77 (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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751 GLY 3.7 9.4 - - - +
761 CYS* 1.3 77.7 - - - +
781 HIS* 1.3 64.3 + - + +
961 TRP* 3.9 21.3 - - + -
981 ILE* 5.7 0.2 - - + -
991 ASN 4.5 4.0 - - - +
1001 LEU* 3.8 25.1 - - + -
1021 GLU* 4.2 10.2 + - - +
1031 MET* 3.4 19.3 + - - +
1061 ILE* 3.6 32.3 - - + -
2361 ILE* 2.9 27.4 + - + +
2381 HIS* 3.7 20.6 - - + -
70021 W02 3.9 26.9 - - + -
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Residues in contact with HIS 78 (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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761 CYS* 3.6 6.2 - - - -
771 ILE* 1.3 84.3 - - - +
791 GLU* 1.3 75.6 + - - +
801 SER* 3.6 29.8 + - - -
961 TRP* 3.3 72.5 + + + +
1021 GLU* 3.6 10.0 + - - -
1031 MET* 3.8 4.9 - - - +
2171 LEU* 5.3 2.7 - - + -
2341 THR 3.9 0.2 - - - +
2351 ARG* 3.4 3.3 - - - -
2361 ILE* 2.9 41.6 + - + -
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Residues in contact with GLU 79 (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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761 CYS* 4.0 4.6 - - - -
781 HIS* 1.3 89.1 + - - +
801 SER* 1.3 62.5 + - - +
811 VAL* 3.8 10.8 + - + +
1031 MET* 3.8 21.7 - - + +
2331 VAL* 4.7 7.2 - - + -
2341 THR 3.7 3.8 - - - -
2351 ARG* 2.7 46.4 + - + +
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Residues in contact with SER 80 (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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781 HIS* 3.6 23.1 + - - -
791 GLU* 1.3 71.7 - - - +
811 VAL* 1.3 60.9 + - - +
821 LEU* 5.0 2.4 - - - +
941 THR* 3.7 22.7 - - - +
1421 TYR* 6.1 0.2 - - - -
2171 LEU* 6.2 1.8 - - - -
2191 SER* 4.2 12.2 + - - -
2321 VAL 3.6 1.3 - - - +
2331 VAL* 3.2 6.6 - - - +
2341 THR* 2.8 54.0 + - - -
2361 ILE* 5.5 1.8 - - - -
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Residues in contact with VAL 81 (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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791 GLU* 3.8 10.7 + - + +
801 SER* 1.3 79.1 + - - +
821 LEU* 1.3 75.9 + - - +
831 ASP* 3.9 15.0 + - + +
941 THR* 4.3 7.3 + - - +
2311 LYS* 3.8 29.6 - - + -
2321 VAL 3.7 1.8 - - - -
2331 VAL* 4.4 16.4 - - + +
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Residues in contact with LEU 82 (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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801 SER* 5.0 2.9 - - - +
811 VAL* 1.3 78.2 - - - +
831 ASP* 1.3 59.5 + - - +
841 ILE* 3.9 3.4 + - - +
911 GLN 3.7 11.2 - - - +
921 SER 4.0 8.1 - - - +
931 PHE 3.6 23.3 - - - +
941 THR* 3.4 31.2 - - + -
1401 MET* 3.8 29.2 - - + -
2191 SER* 4.7 4.5 - - - -
2201 ARG* 4.5 6.7 - - - +
2211 ILE* 3.8 23.7 - - + +
2301 VAL 3.9 1.0 - - - +
2311 LYS* 3.3 2.3 - - - -
2321 VAL* 2.8 47.8 + - + +
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Residues in contact with ASP 83 (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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811 VAL* 3.9 15.5 + - + +
821 LEU* 1.3 71.5 - - - +
841 ILE* 1.3 60.4 + - - +
851 VAL* 3.1 24.5 + - + +
911 GLN* 3.5 17.5 + - - +
1311 LYS* 2.7 40.9 + - - +
2311 LYS* 3.7 23.0 + - + +
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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