Contacts of the strand formed by residues 39 - 45 (chain C) in PDB entry 1QD6
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 TYR 39 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C THR* 3.5 28.0 - - - -
38C ASN* 1.3 75.0 - - - +
40C LEU* 1.3 62.4 + - - +
41C ILE* 4.0 23.1 - - + -
68C LYS* 3.5 28.7 + - + -
69C PHE* 3.2 5.9 - - - +
70C GLN* 3.0 65.6 + - + +
95C LYS* 5.5 1.9 - - - +
224C GLU* 4.3 7.9 + - - -
238C TYR* 3.7 27.8 - + + -
240C GLN* 3.2 25.4 + - - -
263C VAL 3.3 15.3 - - - +
264C MET* 4.1 5.2 - - + -
270D HDS 3.7 9.3 - - - +
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C TYR* 1.3 73.9 - - - +
41C ILE* 1.3 61.5 + - - +
67C VAL* 3.4 33.2 - - + -
68C LYS 3.6 2.7 - - - -
69C PHE* 3.6 15.9 - - + -
98C TRP* 6.1 0.7 - - + -
262C GLY* 3.4 1.7 - - - -
263C VAL* 2.8 45.2 + - + +
270D HDS 3.7 46.4 - - + +
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C TYR* 4.0 12.3 - - + -
40C LEU* 1.3 81.5 - - - +
42C TYR* 1.3 59.0 + - - +
43C THR* 3.7 22.9 - - + -
67C VAL* 3.5 9.6 - - - +
68C LYS* 2.8 43.0 + - + +
238C TYR* 3.6 26.9 - - + +
240C GLN* 3.8 40.6 - - + +
260C GLY* 4.2 5.8 - - - +
261C VAL* 3.3 12.6 - - - +
262C GLY* 3.6 17.5 - - - +
263C VAL 4.4 0.4 - - - +
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Residues in contact with TYR 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ILE* 1.3 74.3 - - - +
43C THR* 1.3 63.8 + - - +
65C ASP* 2.5 42.8 + - + -
66C GLU 3.9 7.4 - - - -
67C VAL* 3.6 28.9 - - + -
100C LEU* 4.6 13.2 - - + -
101C SER* 3.6 14.4 + - - -
259C VAL 4.0 0.2 - - - +
260C GLY* 3.1 1.7 - - - -
261C VAL* 2.7 37.1 + - - +
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Residues in contact with THR 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ILE* 3.7 31.6 - - + -
42C TYR* 1.3 86.3 - - - +
44C GLN* 1.3 62.3 + - - +
65C ASP* 3.2 9.7 - - - +
66C GLU* 2.7 45.5 + - - +
68C LYS* 3.8 16.3 - - + +
240C GLN* 5.5 0.4 - - - +
258C ARG* 2.8 37.6 + - + +
259C VAL 3.1 8.5 - - - -
260C GLY* 3.8 4.5 - - - -
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Residues in contact with GLN 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C THR* 1.3 74.4 - - - +
45C THR* 1.3 65.8 + - - +
64C LYS* 3.5 29.1 - - - +
65C ASP* 3.4 22.5 - - - +
257C THR 3.9 0.9 - - - +
258C ARG* 3.4 4.2 - - - -
259C VAL* 2.9 41.6 + - + +
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Residues in contact with THR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLN* 1.3 81.2 + - - +
46C SER* 1.3 65.0 + - - +
47C ASP 3.3 24.3 + - - +
48C LEU* 4.0 10.1 - - + -
64C LYS* 2.9 46.1 + - - +
256C GLN* 2.8 26.9 + - - +
257C THR 3.4 6.5 + - - -
258C ARG* 3.7 30.8 - - - +
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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