Contacts of the helix formed by residues 300 - 316 (chain D) in PDB entry 2GF2
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 ILE 300 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLU* 3.3 22.4 - - + +
229A LEU* 4.5 5.8 - - + -
308B GLN* 3.0 13.8 + - - +
214D MET* 3.9 34.5 - - + -
289D ALA* 4.5 0.9 - - + +
290D GLN* 3.7 28.7 - - + +
293D ALA* 3.6 28.3 - - + -
298D SER* 4.0 7.0 - - - +
299D PRO* 1.3 77.5 - - - +
301D LEU* 1.3 58.6 + - - +
303D GLY 4.1 4.7 - - - +
304D SER* 2.7 52.4 + - - +
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 3.2 8.0 + - - +
305A LEU* 5.6 1.3 - - + -
309A ILE* 3.7 31.9 - - + -
312A MET* 5.3 0.2 - - + -
329A PHE* 5.9 0.2 - - + -
330A LEU* 4.7 11.7 - - + -
305B LEU* 3.6 30.0 - - + +
308B GLN* 3.8 23.6 - - + -
309B ILE* 4.3 20.2 - - + +
312B MET* 3.8 31.2 - - + -
301C LEU* 4.8 12.3 - - + -
299D PRO* 3.9 2.3 - - + -
300D ILE* 1.3 75.6 - - - +
302D LEU* 1.3 66.3 + - + +
304D SER* 3.8 2.4 - - - -
305D LEU* 3.4 19.8 + - - +
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Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ILE* 3.4 47.6 - - + +
221A ILE* 3.9 19.5 - - + -
222A GLY 4.5 0.2 - - - +
225A GLU* 2.8 24.0 + - - +
302A LEU* 3.7 27.0 - - + +
305A LEU* 3.6 32.5 - - + -
306A ALA 4.3 3.1 - - - +
309A ILE* 4.6 4.5 - - + -
218D ILE* 4.0 15.0 - - + -
301D LEU* 1.3 72.6 - - - +
303D GLY* 1.3 59.2 + - - +
305D LEU* 3.2 5.8 + - + +
306D ALA* 2.9 29.6 + - - +
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Residues in contact with GLY 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLU* 2.9 14.3 + - - -
214D MET* 4.0 18.1 - - - +
218D ILE* 3.6 18.5 - - - +
286D LEU* 4.5 5.5 - - - +
300D ILE* 4.1 8.2 - - - +
301D LEU 3.4 0.2 - - - -
302D LEU* 1.3 78.1 - - - +
304D SER* 1.3 59.3 + - - +
306D ALA* 3.6 3.1 + - - +
307D HIS* 3.1 22.7 + - - +
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Residues in contact with SER 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B SER* 3.8 21.5 - - - -
305B LEU* 5.2 0.9 - - - -
308B GLN* 3.0 16.5 + - - -
290D GLN* 2.8 33.7 + - - +
300D ILE* 2.7 26.9 + - - +
301D LEU 3.8 3.8 - - - -
303D GLY* 1.3 76.3 - - - +
305D LEU* 1.3 57.3 + - - +
307D HIS* 3.3 4.5 + - - +
308D GLN* 3.0 34.1 + - - +
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Residues in contact with LEU 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LEU* 4.0 20.6 - - + +
302A LEU* 3.7 17.0 - - + -
305A LEU* 4.4 11.2 - - + -
301B LEU* 3.1 33.2 - - + +
304B SER* 5.7 1.3 - - - -
305B LEU* 4.4 11.6 - - + +
305C LEU* 3.7 33.9 - - + -
301D LEU 3.4 12.9 + - - +
302D LEU 3.2 7.8 + - - +
304D SER* 1.3 77.2 - - - +
306D ALA* 1.3 59.7 + - - +
308D GLN* 3.2 4.6 + - - +
309D ILE* 2.9 45.9 + - + +
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Residues in contact with ALA 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A LEU* 4.2 2.7 - - + +
217D ALA* 4.2 17.7 - - + -
218D ILE* 4.2 15.0 - - + +
221D ILE* 3.5 26.7 - - + -
286D LEU* 3.9 4.9 - - + -
302D LEU 2.9 17.4 + - - +
303D GLY* 3.6 5.6 - - - +
305D LEU* 1.3 75.5 - - - +
307D HIS* 1.3 61.5 + - - +
309D ILE* 3.4 1.5 + - - +
310D TYR* 3.1 30.7 + - - -
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Residues in contact with HIS 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B THR* 3.4 39.0 - - + +
283D ALA* 4.1 8.5 + - - -
286D LEU* 3.8 24.9 - - + +
287D GLY* 3.7 20.8 - - - -
290D GLN* 2.7 31.5 + - + +
303D GLY 3.1 14.3 + - - +
304D SER 3.3 9.0 - - - +
306D ALA* 1.3 77.0 - - - +
308D GLN* 1.3 68.0 + - - +
310D TYR* 3.4 2.9 + - - +
311D ARG* 2.9 42.5 + - + +
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Residues in contact with GLN 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B GLN* 3.7 6.3 - - - +
293B ALA* 5.4 0.7 - - - +
294B THR* 5.4 0.2 + - - -
298B SER 3.7 5.5 - - - +
299B PRO* 3.4 9.0 - - + +
300B ILE* 2.9 34.6 + - - +
301B LEU* 3.5 26.7 - - + +
304B SER* 3.1 29.4 + - - +
290D GLN* 3.3 8.3 + - - -
304D SER 3.0 17.0 + - - +
305D LEU* 3.2 1.3 + - - +
307D HIS* 1.3 107.9 + - - +
309D ILE* 1.3 57.2 + - - +
311D ARG* 3.4 7.7 - - - +
312D MET* 2.9 34.6 + - - +
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Residues in contact with ILE 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 3.5 43.5 - - + -
302A LEU* 4.4 4.0 - - + -
301B LEU* 4.3 2.5 - - + -
221D ILE* 4.1 29.2 - - + -
305D LEU* 2.9 33.7 + - + +
306D ALA 3.7 4.3 - - - +
308D GLN* 1.3 77.4 - - - +
310D TYR* 1.3 58.7 + - + +
312D MET* 3.3 12.7 + - + +
313D MET* 3.0 31.2 + - - +
326D VAL* 4.0 26.0 - - + -
329D PHE* 4.5 11.1 - - + -
330D LEU* 5.9 2.9 - - + -
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Residues in contact with TYR 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D ALA* 4.0 9.9 - - + -
220D MET* 3.8 6.1 - - - +
221D ILE* 3.5 23.6 - - + +
279D THR* 4.0 12.1 - - + +
282D MET* 3.9 16.8 - - + -
283D ALA* 4.3 14.6 - - + -
286D LEU* 3.6 17.7 - - + -
306D ALA 3.1 25.9 + - - +
307D HIS 4.0 2.7 - - - +
309D ILE* 1.3 73.2 - - + +
311D ARG* 1.3 61.4 + - - +
313D MET* 3.4 25.7 + - + +
314D CYS* 3.0 31.7 + - - -
323D PHE* 2.8 55.3 + + + -
326D VAL* 3.6 16.4 - - + +
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Residues in contact with ARG 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ALA 5.4 0.4 - - - -
294B THR* 5.2 2.5 + - - +
297B LYS* 3.4 70.7 + - - +
298B SER 4.4 1.3 - - - +
299B PRO* 4.0 21.9 - - + +
280D THR* 5.8 4.0 - - - +
283D ALA* 4.0 23.9 + - - +
284D LYS* 5.9 0.2 - - - +
307D HIS* 2.9 29.6 + - + +
308D GLN* 3.4 15.5 - - - +
310D TYR* 1.3 73.2 - - - +
312D MET* 1.3 65.6 + - - +
314D CYS* 3.2 41.5 + - - +
315D ALA* 3.4 10.6 + - - +
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Residues in contact with MET 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LEU* 5.0 0.2 - - + -
299B PRO* 3.8 20.9 - - + -
301B LEU* 3.9 24.7 - - + -
312C MET* 3.8 28.9 - - + -
329C PHE* 4.3 20.2 - - + +
330C LEU* 4.4 11.9 - - - -
308D GLN 2.9 18.0 + - - +
309D ILE* 3.4 16.4 - - + +
311D ARG* 1.3 76.4 - - - +
313D MET* 1.3 62.7 + - - +
315D ALA* 3.0 14.7 + - - +
316D LYS* 2.9 32.2 - - - +
329D PHE* 3.9 22.9 - - + -
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Residues in contact with MET 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D THR* 3.8 17.0 - - + +
309D ILE* 3.0 18.3 + - - +
310D TYR* 3.6 28.7 - - + +
311D ARG 3.3 0.4 - - - -
312D MET* 1.3 76.8 - - - +
314D CYS* 1.3 60.9 + - - +
316D LYS* 3.2 8.1 + - - -
318D TYR* 3.1 43.8 + - + +
325D SER* 3.4 26.5 - - - +
326D VAL* 3.6 42.4 - - - +
329D PHE* 3.7 24.5 - - + -
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Residues in contact with CYS 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D THR* 3.8 19.1 - - - -
280D THR* 4.0 17.3 - - - -
283D ALA* 3.9 13.2 - - - -
310D TYR 3.0 19.7 + - - -
311D ARG* 3.4 36.3 - - - +
312D MET 3.2 0.2 - - - -
313D MET* 1.3 77.4 - - - +
315D ALA* 1.3 59.7 + - - +
316D LYS 3.6 0.5 + - - -
317D GLY* 4.2 3.8 + - - -
319D SER* 3.9 22.2 + - - +
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Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C LEU 5.6 5.6 - - - +
331C ARG 5.5 8.5 - - - +
311D ARG 3.4 7.2 + - - +
312D MET* 3.0 11.9 + - - +
314D CYS* 1.3 77.0 - - - +
316D LYS* 1.3 67.4 + - + +
317D GLY 3.6 1.1 + - - -
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Residues in contact with LYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C LYS* 5.9 2.5 - - + -
318C TYR* 5.3 1.2 + - - -
328C GLN 4.9 1.4 + - - -
329C PHE* 2.4 57.5 + - + +
330C LEU* 4.8 3.2 + - - +
331C ARG 5.2 4.6 - - - -
312D MET* 2.9 37.5 - - - +
313D MET 3.2 5.7 + - - +
315D ALA* 1.3 87.7 - - - +
317D GLY* 1.3 59.8 + - - +
318D TYR* 3.5 24.0 - - + -
329D PHE* 4.1 14.8 - - + -
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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