Contacts of the strand formed by residues 255 - 264 (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 ASN 255 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C SER* 4.9 0.5 + - - -
47C ASP* 5.2 2.9 - - - +
243C SER* 5.0 1.2 + - - -
244C GLY* 3.2 26.8 + - - -
245C TYR* 3.5 34.7 + - + +
254C PHE* 1.3 87.5 - - - +
256C GLN* 1.3 71.5 + - - +
257C THR* 5.4 0.3 + - - -
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Residues in contact with GLN 256 (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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45C THR* 2.8 29.2 + - - +
46C SER* 3.5 10.1 - - - +
47C ASP 3.6 6.7 - - - +
48C LEU* 5.2 2.6 - - - +
49C ASN 5.5 0.2 + - - -
110C ARG* 5.2 0.3 + - - -
242C TYR* 3.9 3.0 - - + +
243C SER* 3.4 2.4 - - - -
244C GLY 3.0 30.3 + - - +
247C GLU* 3.5 28.5 + - + +
251C ASP* 3.0 41.2 + - - +
254C PHE* 3.8 18.0 + - + -
255C ASN* 1.3 79.8 + - - +
257C THR* 1.3 64.7 + - - +
258C ARG* 3.5 13.7 + - + +
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Residues in contact with THR 257 (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 3.9 1.0 - - - +
45C THR* 3.4 1.6 - - - -
46C SER* 2.7 44.6 + - - -
241C VAL* 4.5 13.0 - - + -
242C TYR 3.2 11.0 - - - +
243C SER* 2.8 24.4 + - - +
255C ASN* 5.4 0.3 + - - -
256C GLN* 1.3 71.9 - - - +
258C ARG* 1.3 64.0 + - - +
259C VAL* 4.4 1.5 + - + -
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Residues in contact with ARG 258 (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* 2.8 34.6 + - + -
44C GLN 3.4 8.5 - - - +
45C THR* 3.7 16.9 - - - +
48C LEU* 4.6 0.8 - - - +
64C LYS 3.8 13.3 + - - -
66C GLU* 2.5 47.1 + - - +
68C LYS* 4.7 2.7 - - - +
97C TRP* 3.8 8.5 - - - +
110C ARG* 3.6 9.7 - - - +
240C GLN* 4.0 3.4 + - - +
241C VAL* 3.3 5.4 - - - +
242C TYR* 2.7 49.9 + - + +
247C GLU* 3.3 37.8 + - - +
256C GLN* 3.5 18.3 + - + +
257C THR* 1.3 77.0 - - - +
259C VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 259 (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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42C TYR 4.0 0.2 - - - +
43C THR* 3.1 5.6 - - - -
44C GLN* 2.9 45.8 + - + +
239C THR* 5.0 6.3 - - + -
240C GLN 3.4 8.7 - - - +
241C VAL* 4.2 16.4 - - + -
257C THR* 4.4 1.3 + - + -
258C ARG* 1.3 75.3 - - - +
260C GLY* 1.3 66.1 + - - +
261C VAL* 5.5 3.4 - - + -
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Residues in contact with GLY 260 (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* 4.2 9.2 - - - +
42C TYR 3.1 11.9 - - - -
43C THR* 3.8 11.2 - - - -
239C THR* 3.3 5.0 - - - +
240C GLN* 2.8 37.8 + - - +
259C VAL* 1.3 78.9 - - - +
261C VAL* 1.3 67.6 + - - +
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Residues in contact with VAL 261 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C ILE* 3.7 5.1 - - - +
42C TYR* 2.7 37.1 + - + +
237C LEU* 6.4 2.0 - - + -
238C TYR 3.4 9.4 - - - +
239C THR* 3.7 20.2 - - + +
259C VAL* 5.5 4.5 - - + -
260C GLY* 1.3 80.1 - - - +
262C GLY* 1.3 65.7 + - - +
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C LEU 3.4 10.5 - - - -
41C ILE* 3.6 4.1 - - - +
237C LEU* 3.6 11.1 - - - +
238C TYR 2.8 31.9 + - - +
261C VAL* 1.3 80.9 - - - +
263C VAL* 1.3 66.5 + - - +
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Residues in contact with VAL 263 (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* 3.3 6.1 - - - +
40C LEU* 2.8 43.6 + - + +
41C ILE* 4.5 0.3 - - - +
231C ILE* 4.3 11.4 - - + -
235C VAL* 4.1 16.2 - - + -
236C ARG 3.2 10.5 - - - +
237C LEU* 4.7 3.6 - - + -
238C TYR* 4.2 3.1 - - - +
262C GLY* 1.3 79.3 - - - +
264C MET* 1.3 61.6 + - - +
270D HDS 3.2 31.6 - - + -
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Residues in contact with MET 264 (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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37C THR* 3.9 21.1 - - + -
38C ASN 3.4 9.2 - - - +
39C TYR* 4.1 5.8 - - + +
228C SER* 3.8 12.6 - - - -
235C VAL* 3.5 5.8 - - - +
236C ARG* 2.7 39.3 + - + +
238C TYR* 3.7 45.3 - - + +
263C VAL* 1.3 76.9 - - - +
265C LEU* 1.3 69.1 + - - +
266C ASN 3.5 13.5 - - - +
267C ASP* 3.4 44.6 - - - +
270D HDS 5.0 0.9 - - - -
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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