Contacts of the strand formed by residues 227 - 238 (chain A) in PDB entry 1QFG
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 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A TRP* 4.9 4.5 - - + +
222A ARG* 3.4 16.3 - - - +
223A PRO* 3.4 26.9 - - + -
224A ASP* 2.8 33.4 + - - +
225A ASP 3.4 1.2 - - - -
226A LYS* 1.3 85.3 + - - +
228A ASN* 1.3 67.6 + - - +
229A PHE 5.0 0.2 - - - +
286A PHE* 4.2 21.1 - - + -
287A ASP* 3.6 4.3 - - - +
288A HIS* 3.7 20.5 + - + +
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Residues in contact with ASN 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A THR* 4.0 9.6 + - - +
221A TRP 3.7 3.8 - - - -
222A ARG* 3.4 29.9 - - - +
227A THR* 1.3 78.5 - - - +
229A PHE* 1.3 63.7 + - - +
230A THR* 2.8 28.7 + - - -
285A SER* 4.2 1.0 - - - +
286A PHE* 3.2 8.5 - - - -
287A ASP* 2.9 60.9 + - - +
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Residues in contact with PHE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A PHE* 3.7 5.2 - + - +
220A THR* 3.5 1.2 - - - -
221A TRP* 2.9 61.0 + + + -
227A THR* 5.0 0.2 - - - +
228A ASN* 1.3 77.2 + - - +
230A THR* 1.3 58.3 + - - +
231A PHE* 4.2 21.1 - - + -
284A TYR* 3.4 36.6 - + + -
285A SER 3.5 2.2 - - - -
286A PHE* 3.9 21.8 - + + -
1011A FTT 3.7 26.9 - - + -
1012A DAO 4.3 12.1 - - + -
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ARG* 4.4 20.2 + - + +
156A PRO* 4.0 13.5 - - + -
219A PHE 3.3 6.3 - - - +
220A THR* 2.9 25.1 + - - +
228A ASN* 2.8 24.2 + - - -
229A PHE* 1.3 72.8 - - - +
231A PHE* 1.3 63.3 + - - +
232A LEU* 3.5 25.4 + - + +
284A TYR* 3.1 5.8 - - - -
285A SER* 2.7 41.1 + - - -
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Residues in contact with PHE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A PRO* 4.0 7.6 - - + -
218A ALA* 3.1 10.7 - - - +
219A PHE* 2.6 53.9 + - + +
229A PHE* 4.0 15.0 + - + -
230A THR* 1.3 70.7 - - - +
232A LEU* 1.3 60.4 + - - +
233A SER* 3.8 29.6 - - - -
282A VAL* 4.3 15.0 - - + -
283A GLY 3.2 23.1 - - - -
284A TYR* 4.0 2.7 - - - -
1011A FTT 4.1 19.3 - - + -
1013A FTT 3.5 41.1 - - + -
1014A MYR 3.8 18.4 - - + -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASN* 3.5 34.5 - - + +
153A SER* 3.8 14.6 - - - +
154A LYS 4.2 6.3 - - - +
155A ARG* 3.7 38.6 - - - +
217A PRO 4.3 0.7 - - - -
218A ALA* 4.3 5.8 - - + +
230A THR* 3.5 19.9 + - + +
231A PHE* 1.3 77.5 - - - +
233A SER* 1.3 60.7 + - - +
281A MET* 4.6 0.9 - - - +
282A VAL* 3.7 1.6 + - - -
283A GLY* 3.0 35.9 + - - +
284A TYR 4.5 2.9 - - - +
285A SER* 4.2 17.9 - - - +
301A ARG* 5.8 1.6 - - - -
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Residues in contact with SER 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ALA* 3.3 22.1 - - - +
217A PRO* 2.5 50.2 + - - +
218A ALA* 5.3 0.2 - - - +
231A PHE* 3.8 20.8 - - - -
232A LEU* 1.3 76.1 - - - +
234A TYR* 1.3 63.9 + - - +
235A PHE* 3.6 11.1 - - - -
281A MET* 3.3 14.6 - - - -
282A VAL* 4.3 1.6 - - - -
1014A MYR 4.9 0.2 - - - +
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Residues in contact with TYR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 5.8 2.2 - - + -
121A ILE* 3.4 30.5 - - + -
122A ASP* 2.7 28.8 + - - +
125A MET* 3.4 32.8 - - + -
214A ALA* 4.2 6.6 - - + +
215A ILE 3.8 3.1 - - - -
216A ALA* 3.8 17.9 - - + -
233A SER* 1.3 73.6 - - - +
235A PHE* 1.3 65.6 + - - +
236A GLN* 2.5 41.1 + - + -
279A GLU* 3.7 12.5 - - + +
280A LYS* 3.3 2.4 - - - -
281A MET* 2.9 62.0 + - + +
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Residues in contact with PHE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A TYR 3.9 0.2 - - - +
214A ALA* 3.4 3.3 - - - +
215A ILE* 2.9 56.8 + - + +
217A PRO* 4.0 10.3 - - + -
233A SER* 3.6 28.5 - - - -
234A TYR* 1.3 77.7 - - - +
236A GLN* 1.3 59.4 - - - +
279A GLU 3.3 3.4 - - - +
280A LYS* 3.5 34.3 - - + -
281A MET 3.9 13.5 - - - -
282A VAL* 4.2 9.0 - - + -
1014A MYR 4.2 36.3 - - + -
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Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A VAL* 3.5 10.4 + - - +
122A ASP 4.1 0.2 + - - -
212A ARG* 3.8 26.1 + - + +
213A TYR 3.1 12.3 - - - +
214A ALA* 3.9 5.4 - - + +
234A TYR* 2.5 38.6 + - + -
235A PHE* 1.3 75.0 - - - +
237A ASN* 1.3 62.6 + - - +
238A GLU* 3.2 34.2 + - + +
277A ARG 4.8 0.4 - - - +
278A ASN* 3.6 6.1 + - - -
279A GLU* 2.6 70.6 + - + +
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Residues in contact with ASN 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ARG* 3.6 0.7 - - - -
213A TYR* 2.8 55.0 + - + +
236A GLN* 1.3 71.9 - - - +
238A GLU* 1.3 69.4 + - - +
239A PRO* 3.7 23.5 - - - +
277A ARG 4.0 1.8 - - - +
278A ASN* 3.1 22.4 + - - +
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLN 3.5 15.2 - - - +
212A ARG* 2.9 35.5 + - + +
236A GLN* 3.2 23.2 + - + +
237A ASN* 1.3 82.1 - - - +
239A PRO* 1.3 65.0 - - - +
240A GLU* 3.4 2.4 - - - +
241A THR* 4.3 13.8 + - - +
276A SER* 3.2 6.9 - - - -
277A ARG* 2.7 84.3 + - - +
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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