Contacts of the strand formed by residues 274 - 289 (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 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PRO 4.7 1.9 + - - -
240A GLU* 2.7 27.3 + - - -
272A ASN 4.0 5.8 - - - +
273A ASN* 1.3 77.1 - - - +
275A TYR* 1.3 61.2 + - - +
276A SER* 5.5 1.6 - - - -
308A SER* 6.4 0.7 - - - -
309A GLN* 2.9 9.3 - - - +
310A ASN* 2.7 71.0 + - + +
311A SER* 4.0 1.0 + - - -
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Residues in contact with TYR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 4.1 11.2 - - + -
87A TYR* 2.9 29.6 + - - -
116A TYR* 3.1 13.0 - - + -
239A PRO 3.1 8.0 - - - +
240A GLU* 3.1 9.5 + - - +
241A THR* 2.8 46.2 + - + +
242A GLY 4.4 12.6 - - - +
244A TYR* 3.9 30.5 - + + -
274A THR* 1.3 74.6 + - - +
276A SER* 1.3 65.7 + - - +
277A ARG* 6.2 1.1 - - + -
307A THR* 3.9 16.8 - - - -
308A SER 3.6 6.3 - - - -
309A GLN* 3.0 44.3 + - + -
311A SER* 4.0 6.1 - - - +
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLU 3.2 8.3 - - - -
239A PRO* 2.9 25.1 - - - -
241A THR* 4.3 3.6 - - - -
274A THR* 5.5 1.6 - - - -
275A TYR* 1.3 74.4 - - - +
277A ARG* 1.3 58.4 + - - +
307A THR* 2.6 28.2 + - - -
308A SER* 2.8 42.6 + - - -
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Residues in contact with ARG 277 (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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85A ASN 4.9 0.6 + - - -
86A THR* 2.9 38.0 + - - +
87A TYR* 3.3 18.3 + - - -
116A TYR 5.9 0.2 - - - -
117A ASN* 5.4 2.5 - - - +
118A ASP 2.9 27.8 + - - -
119A ALA* 4.4 0.2 - - - +
120A VAL* 3.2 24.4 - - - +
212A ARG* 4.2 1.2 - - - +
236A GLN 4.3 0.2 - - - +
237A ASN* 3.9 2.0 - - - +
238A GLU* 2.7 74.7 + - - +
241A THR* 4.2 10.5 + - - +
275A TYR* 6.2 1.1 - - + -
276A SER* 1.3 73.8 - - - +
278A ASN* 1.3 66.7 + - - +
279A GLU* 3.2 24.6 + - + +
305A ASN* 5.7 0.9 - - + -
306A LYS 3.2 10.5 - - - +
307A THR* 4.5 8.7 - - - +
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Residues in contact with ASN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLN 3.6 10.5 + - - -
237A ASN* 3.1 29.2 + - - +
277A ARG* 1.3 74.6 - - - +
279A GLU* 1.3 64.2 + - - +
280A LYS* 3.6 33.1 + - - +
304A GLU 5.1 1.0 - - - +
305A ASN* 3.1 6.8 - - - +
306A LYS* 2.6 63.6 + - + +
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ALA* 3.2 14.2 - - + +
120A VAL 2.5 46.6 + - - +
234A TYR* 3.7 11.1 - - + -
235A PHE* 3.3 1.4 - - - +
236A GLN* 2.6 65.6 + - + +
277A ARG* 3.2 28.9 + - + -
278A ASN* 1.3 76.8 - - - +
280A LYS* 1.3 65.0 + - - +
281A MET* 4.3 8.4 - - + +
305A ASN* 3.2 17.3 - - + +
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Residues in contact with LYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR 3.3 6.3 - - - -
235A PHE* 3.5 23.1 - - + -
278A ASN* 3.6 21.9 + - - +
279A GLU* 1.3 76.4 - - - +
281A MET* 1.3 62.6 + - - +
303A ALA* 3.3 4.7 - - - +
304A GLU* 2.9 46.6 + - + +
305A ASN* 3.4 1.0 + - - -
306A LYS* 4.3 16.6 - - - +
1014A MYR 4.1 34.0 + - + +
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Residues in contact with MET 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.2 10.3 - - - -
111A LEU* 3.4 33.4 - - + -
119A ALA* 4.5 3.8 - - + -
121A ILE* 4.0 14.6 - - + -
232A LEU 4.6 0.7 - - - +
233A SER* 3.3 5.9 - - - -
234A TYR* 2.9 58.5 + - + +
235A PHE* 3.9 3.1 - - - -
279A GLU* 4.3 11.7 - - + +
280A LYS* 1.3 78.4 - - - +
282A VAL* 1.3 69.2 + - - +
301A ARG* 4.0 22.4 - - - -
302A PHE 3.2 11.4 - - - +
303A ALA* 4.2 6.3 - - + -
305A ASN* 4.4 13.7 - - - +
1014A MYR 5.9 1.3 - - - -
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 4.3 11.9 - - + -
232A LEU 3.7 5.6 - - - -
233A SER* 4.3 5.6 - - - -
235A PHE* 4.2 10.8 - - + -
281A MET* 1.3 81.1 - - - +
283A GLY* 1.3 54.8 + - - +
301A ARG* 3.6 3.0 - - - -
302A PHE* 2.7 43.5 + - + +
1011A FTT 3.9 18.1 - - + +
1013A FTT 3.6 27.6 - - + -
1014A MYR 3.9 38.1 - - + -
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.2 13.9 - - - -
232A LEU* 3.0 29.3 + - - -
282A VAL* 1.3 75.0 - - - +
284A TYR* 1.3 68.9 - - - +
300A LEU* 3.0 22.2 - - - -
301A ARG* 4.0 4.5 - - - -
1011A FTT 4.3 4.9 - - - +
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Residues in contact with TYR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 3.4 28.3 - + + -
230A THR 3.1 15.9 - - - +
231A PHE* 4.0 0.2 - - - -
232A LEU* 4.0 10.5 - - - +
283A GLY* 1.3 74.1 - - - +
285A SER* 1.3 62.2 + - - +
286A PHE* 4.1 15.5 - + + -
298A GLN* 2.7 36.9 + - - -
299A ASN* 3.7 1.9 - - - +
300A LEU* 3.0 71.6 + - + +
1009A FTT 3.9 3.6 - - - +
1011A FTT 3.5 21.3 - - + -
1012A DAO 3.8 34.2 - - + +
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASN* 6.0 1.1 - - - -
155A ARG* 4.0 33.5 + - - -
228A ASN* 3.6 2.5 - - - +
229A PHE* 3.5 1.9 - - - -
230A THR* 2.7 37.2 + - - +
232A LEU* 4.2 6.4 - - - +
284A TYR* 1.3 76.5 - - - +
286A PHE* 1.3 62.9 + - - +
287A ASP* 4.5 8.2 + - - -
299A ASN* 3.3 19.1 + - - -
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Residues in contact with PHE 286 (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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221A TRP* 6.2 2.7 - + - -
227A THR* 4.2 16.2 - - + -
228A ASN 3.2 17.3 - - - -
229A PHE* 3.9 18.8 - + + -
284A TYR* 4.1 15.3 - + + -
285A SER* 1.3 78.5 + - - +
287A ASP* 1.3 72.0 + - - +
288A HIS* 3.8 31.2 - - + -
296A VAL* 4.5 12.1 - - + -
297A ARG* 3.0 23.1 - - - +
298A GLN* 3.0 38.1 + - + +
299A ASN* 4.3 0.4 + - - +
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Residues in contact with ASP 287 (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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226A LYS 4.4 2.0 - - - +
227A THR* 3.6 2.1 + - - -
228A ASN* 2.9 64.1 + - - +
285A SER* 4.5 7.3 + - - -
286A PHE* 1.3 83.8 - - - +
288A HIS* 1.3 62.4 + - - +
295A THR* 5.2 5.2 - - + -
296A VAL 3.4 5.2 - - - +
297A ARG* 4.0 17.0 - - + +
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Residues in contact with HIS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LYS* 3.1 11.6 - - - +
227A THR* 3.7 16.9 + - - +
286A PHE* 3.8 20.4 - - + -
287A ASP* 1.3 77.5 - - - +
289A GLU* 1.3 83.8 + - - +
290A PHE* 3.4 39.4 + + - -
295A THR* 3.2 5.1 - - - +
296A VAL* 2.6 49.4 + - + +
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Residues in contact with GLU 289 (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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225A ASP 5.4 1.2 - - - +
226A LYS* 2.8 50.6 + - + +
287A ASP 4.4 0.2 - - - -
288A HIS* 1.3 82.2 + - - +
290A PHE* 1.3 59.0 + - - +
291A ASN* 3.6 24.6 - - - +
292A ASP* 5.0 3.6 - - - +
294A PHE 3.9 0.2 - - - -
295A THR* 3.7 24.7 + - + +
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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