Contacts of the helix formed by residues 326 - 349 (chain A) in PDB entry 2GFP
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 GLU 326 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ASN* 5.8 9.1 - - - +
209A PHE* 6.1 0.3 - - - +
210A ASN* 6.4 2.0 - - + -
310A PHE* 3.6 27.8 - - + -
314A GLY* 4.9 9.2 - - - -
319A LEU* 3.9 31.0 - - - +
322A SER 2.9 17.5 + - - +
323A GLY* 3.0 7.4 + - - +
325A MET* 1.3 75.6 - - - +
327A PRO* 1.4 76.0 - - + +
330A PHE* 2.8 43.3 + - + +
331A LEU* 3.4 3.9 + - - +
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Residues in contact with PRO 327 (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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307A ALA* 6.4 0.4 - - - -
310A PHE* 3.8 39.5 - - + +
311A PHE* 6.3 0.2 - - - -
314A GLY* 5.8 1.6 - - - -
315A MET* 5.4 4.7 - - + -
323A GLY* 2.7 25.6 - - - +
324A ALA 4.4 0.4 - - - +
326A GLU* 1.4 94.4 - - + +
328A PHE* 1.3 81.7 + - + +
331A LEU* 2.8 45.6 - - + +
332A ALA 3.9 0.2 + - - -
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Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 4.2 14.8 - + - -
57A GLY* 4.7 4.9 - - - +
60A GLN* 3.5 54.7 - - + -
61A LEU* 3.9 26.9 - - + +
311A PHE* 4.8 3.8 - + - -
315A MET* 3.8 35.0 - - + -
324A ALA* 3.1 31.3 + - + -
327A PRO* 1.3 86.2 - - + +
329A PRO* 1.4 77.0 - - + +
332A ALA* 3.0 32.0 + - - +
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Residues in contact with PRO 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.5 31.0 - - + -
324A ALA 2.7 28.0 - - - +
325A MET* 3.0 20.0 - - + +
328A PHE* 1.4 80.0 - - + +
330A PHE* 1.3 64.0 + - + +
332A ALA* 4.9 1.8 - - + -
333A GLY* 2.8 28.8 + - - +
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 4.7 18.8 - - + -
206A ASN* 5.1 3.4 - - - -
210A ASN* 3.3 32.1 - - + -
214A LEU* 3.3 20.4 - - + +
325A MET* 2.9 47.9 + - + -
326A GLU* 2.8 30.7 + - + +
329A PRO* 1.3 77.5 - - + +
331A LEU* 1.3 58.9 + - + +
333A GLY* 3.6 0.5 - - - -
334A THR* 2.7 30.8 + - - -
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Residues in contact with LEU 331 (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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210A ASN* 5.2 2.0 - - - +
213A LEU* 3.5 51.8 - - + +
214A LEU* 3.9 10.8 - - + +
217A ILE* 2.9 30.7 - - + +
307A ALA* 6.5 1.3 - - + -
310A PHE* 4.0 10.3 - - + -
326A GLU 3.4 11.9 - - - +
327A PRO* 2.8 36.3 + - + +
330A PHE* 1.3 75.3 - - + +
332A ALA* 1.3 54.9 + - - +
334A THR* 2.7 30.6 + - - -
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Residues in contact with ALA 332 (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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53A LEU* 4.6 14.1 - - + +
57A GLY* 4.0 27.1 - - - -
217A ILE* 3.9 6.7 - - - +
327A PRO 3.9 0.2 + - - -
328A PHE* 3.0 22.2 + - - +
329A PRO* 4.4 1.8 - - + +
331A LEU* 1.3 75.2 - - - +
333A GLY* 1.3 61.1 + - - +
335A ALA* 3.2 8.7 + - - +
336A GLY* 3.0 17.8 + - - -
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Residues in contact with GLY 333 (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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329A PRO 2.8 22.8 + - - -
330A PHE 3.6 0.7 - - - -
332A ALA* 1.3 74.9 - - - +
334A THR* 1.3 64.2 + - - +
336A GLY* 3.0 11.9 + - - -
337A ALA* 3.0 12.9 + - - +
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Residues in contact with THR 334 (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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214A LEU* 2.9 58.5 + - + +
215A MET* 4.3 8.5 - - + +
218A GLY* 3.6 16.3 - - - -
330A PHE 2.7 17.4 + - - -
331A LEU 2.7 10.2 + - - -
333A GLY* 1.3 71.1 - - - +
335A ALA* 1.3 61.5 + - - -
337A ALA* 3.1 19.3 + - + +
338A LEU* 3.1 13.5 + - + +
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Residues in contact with ALA 335 (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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53A LEU* 3.3 40.4 - - + -
217A ILE* 3.5 10.0 - - + +
218A GLY* 4.0 1.6 - - - -
221A ALA* 3.8 17.0 - - + +
331A LEU 3.1 2.2 + - - -
332A ALA 3.2 10.3 - - - +
334A THR* 1.3 78.4 - - - +
336A GLY* 1.3 63.8 + - - +
338A LEU* 3.2 4.5 + - - +
339A VAL* 3.0 30.5 + - + +
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Residues in contact with GLY 336 (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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332A ALA 3.0 13.4 + - - -
333A GLY* 3.0 5.1 + - - -
335A ALA* 1.3 76.1 - - - +
337A ALA* 1.3 61.9 + - - +
339A VAL* 3.2 10.1 + - - +
340A GLY* 3.0 20.4 + - - -
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Residues in contact with ALA 337 (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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333A GLY 3.0 11.4 + - - +
334A THR* 3.1 16.5 + - + +
336A GLY* 1.3 74.4 - - - +
338A LEU* 1.3 66.0 + - + +
340A GLY* 3.2 4.9 + - - -
341A GLY* 3.1 16.6 + - - -
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Residues in contact with LEU 338 (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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218A GLY 3.3 34.1 - - - +
219A GLY* 4.1 8.3 - - - +
221A ALA* 4.0 4.9 - - + -
222A GLY* 3.8 22.9 - - - +
334A THR* 3.1 7.0 + - + +
335A ALA 3.7 4.7 - - - +
337A ALA* 1.3 80.1 - - + +
339A VAL* 1.3 63.3 + - - +
341A GLY* 3.0 7.3 + - - +
342A LEU* 2.9 25.7 + - + +
345A ILE* 6.2 3.1 - - + -
361A GLY* 6.2 4.3 - - - -
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Residues in contact with VAL 339 (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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47A SER* 4.7 17.0 + - - +
50A GLY* 3.5 36.8 - - - +
221A ALA* 4.4 11.0 - - + -
335A ALA* 3.0 27.0 + - + +
336A GLY* 3.4 10.5 - - - +
338A LEU* 1.3 76.5 - - - +
340A GLY* 1.3 63.7 + - - +
342A LEU* 2.9 32.4 + - + +
343A GLN* 3.1 6.2 + - - +
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Residues in contact with GLY 340 (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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336A GLY 3.0 13.8 + - - -
337A ALA 3.2 4.0 + - - -
339A VAL* 1.3 73.7 - - - +
341A GLY* 1.3 66.7 + - - +
343A GLN* 2.9 35.8 + - - +
344A ASN* 3.4 4.9 + - - +
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Residues in contact with GLY 341 (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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337A ALA 3.1 9.1 + - - -
338A LEU* 3.0 11.2 + - - -
340A GLY* 1.3 75.9 - - - +
342A LEU* 1.3 50.6 + - - +
344A ASN* 3.3 4.1 + - - +
345A ILE* 2.6 39.8 + - - +
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Residues in contact with LEU 342 (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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43A GLY 6.0 0.2 - - - +
46A GLN* 4.3 29.8 - - + +
47A SER* 5.1 4.5 - - - +
50A GLY 6.0 0.2 - - - +
221A ALA 4.5 8.5 - - - +
222A GLY* 4.6 6.5 - - - +
225A ALA* 3.9 31.9 - - + -
338A LEU* 2.9 17.1 + - + +
339A VAL* 2.9 32.9 + - + +
341A GLY* 1.3 73.4 - - - +
343A GLN* 1.3 66.5 + - - +
345A ILE* 2.9 45.0 + - + +
346A GLY* 3.0 3.5 + - - -
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Residues in contact with GLN 343 (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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47A SER* 5.5 6.2 + - - +
339A VAL 3.1 7.2 + - - +
340A GLY* 2.9 23.2 + - - +
342A LEU* 1.3 78.1 - - - +
344A ASN* 1.3 76.4 + - - +
346A GLY* 3.6 1.0 + - - -
347A SER* 3.3 21.0 + - - +
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Residues in contact with ASN 344 (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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340A GLY 3.4 3.5 + - - +
341A GLY* 3.3 6.3 + - - +
343A GLN* 1.3 94.9 - - + +
345A ILE* 1.3 58.6 + - - +
346A GLY 3.3 0.2 - - - -
347A SER* 3.8 18.1 + - - -
348A GLY* 2.8 27.5 + - - -
357B LEU* 5.0 11.8 - - - +
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Residues in contact with ILE 345 (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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338A LEU* 6.2 3.8 - - + -
341A GLY 2.6 22.4 + - - +
342A LEU* 2.9 39.9 + - + +
344A ASN* 1.3 73.2 - - - +
346A GLY* 1.3 57.5 + - - +
348A GLY* 3.2 1.4 - - - -
349A VAL* 2.5 47.0 + - + +
357A LEU* 5.6 2.9 - - + +
358A PRO* 4.6 26.5 - - + -
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Residues in contact with GLY 346 (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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43A GLY* 6.2 4.7 - - - -
342A LEU 3.0 6.8 + - - -
343A GLN 4.2 1.1 - - - -
345A ILE* 1.3 82.2 - - - +
347A SER* 1.3 53.4 + - - +
348A GLY 2.8 6.2 + - - -
349A VAL* 2.7 40.2 + - - +
350A LEU* 3.7 3.3 + - - +
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Residues in contact with SER 347 (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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343A GLN* 3.3 17.4 + - - +
344A ASN* 3.5 21.0 + - - -
345A ILE 3.5 0.4 - - - -
346A GLY* 1.3 73.9 - - - +
348A GLY* 1.3 56.1 + - - +
350A LEU* 4.6 9.4 - - - +
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Residues in contact with GLY 348 (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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344A ASN* 2.8 16.5 + - - -
345A ILE 3.2 2.0 - - - -
347A SER* 1.3 75.3 - - - +
349A VAL* 1.3 58.0 + - - +
350A LEU* 3.0 14.0 + - - +
351A ALA* 4.3 3.8 + - - +
357A LEU* 5.6 2.9 - - - +
348B GLY 5.8 0.5 - - - +
351B ALA* 6.2 4.3 - - - -
357B LEU* 6.2 4.5 - - - -
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Residues in contact with VAL 349 (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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345A ILE* 2.5 28.9 + - + +
346A GLY* 2.7 27.4 + - - +
348A GLY* 1.3 70.7 - - - +
350A LEU* 1.3 52.1 + - - +
351A ALA* 2.5 21.6 + - - -
352A SER* 4.1 0.9 + - - -
354A SER* 3.0 34.9 + - - -
357A LEU* 5.3 5.8 - - + -
358A PRO* 4.0 21.1 - - + -
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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