Contacts of the helix formed by residues 300 - 315 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A MET* 3.9 37.2 - - + -
289A ALA* 4.2 1.8 - - + +
290A GLN* 3.6 32.3 - - - +
293A ALA* 3.6 26.9 - - + -
298A SER* 4.0 7.6 - - - +
299A PRO* 1.3 78.3 - - - +
301A LEU* 1.3 57.7 + - - +
303A GLY 4.1 2.2 - - - -
304A SER* 2.7 51.7 + - - +
308C GLN* 2.9 16.2 + - - +
225D GLU* 3.4 23.8 - - + +
229D LEU* 4.7 6.3 - - + -
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PRO* 3.8 2.2 + - + -
300A ILE* 1.3 76.1 - - - +
302A LEU* 1.3 64.2 + - - +
304A SER* 3.8 2.9 - - - -
305A LEU* 3.4 18.2 + - - +
301B LEU* 4.5 6.5 - - + -
305C LEU* 3.8 21.0 - - + +
308C GLN* 2.9 48.0 - - + +
309C ILE 4.4 0.2 - - - +
312C MET* 3.9 31.4 - - + -
225D GLU* 3.1 10.1 + - - +
305D LEU* 4.0 16.1 - - + +
309D ILE* 3.5 38.1 - - + -
312D MET* 5.0 0.7 - - + -
329D PHE* 6.0 0.2 - - + -
330D LEU* 5.2 7.9 - - + -
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 3.8 22.1 - - + +
301A LEU* 1.3 70.8 - - - +
303A GLY* 1.3 58.4 + - - +
305A LEU* 3.4 0.7 + - - -
306A ALA* 2.9 30.1 + - - +
218D ILE* 3.2 40.2 - - + +
221D ILE* 3.8 19.5 - - + -
222D GLY 4.1 1.6 - - - +
225D GLU* 2.7 22.5 + - - +
302D LEU* 3.7 28.0 - - + +
305D LEU* 3.7 32.3 - - + -
306D ALA 4.2 5.6 - - - +
309D ILE* 4.4 5.6 - - + -
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Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A MET* 3.9 18.6 - - - -
218A ILE* 3.6 16.1 - - - +
286A LEU* 4.7 4.9 - - - +
300A ILE* 3.6 7.9 + - - +
301A LEU 3.4 0.2 - - - -
302A LEU* 1.3 73.7 - - - +
304A SER* 1.3 59.1 + - - +
306A ALA* 3.4 2.9 + - - +
307A HIS* 3.0 28.4 + - - +
225D GLU* 2.8 16.3 + - - -
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Residues in contact with SER 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLN* 2.7 34.6 + - - +
300A ILE* 2.7 26.0 + - - +
301A LEU 3.8 4.5 - - - -
303A GLY* 1.3 74.0 - - - +
305A LEU* 1.3 60.2 + - - +
307A HIS* 3.2 4.7 - - - +
308A GLN* 3.0 33.9 + - - +
304C SER* 3.8 20.4 - - - -
305C LEU* 5.2 0.7 - - - -
308C GLN* 3.1 15.7 + - - -
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU 3.4 11.2 + - - +
302A LEU 3.4 3.0 + - - +
304A SER* 1.3 76.3 - - - +
306A ALA* 1.3 60.4 + - - +
308A GLN* 3.2 3.0 + - - +
309A ILE* 2.9 39.4 + - + +
305B LEU* 5.4 9.2 - - + -
301C LEU* 4.5 17.3 - - + +
304C SER* 5.8 1.1 - - - -
301D LEU* 5.6 1.1 - - + -
302D LEU* 3.6 21.8 - - + -
305D LEU* 4.4 11.7 - - + -
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ALA* 4.0 19.3 - - + -
218A ILE* 4.2 12.3 - - + -
221A ILE* 3.5 28.7 - - + -
286A LEU* 3.9 4.0 - - + -
302A LEU 2.9 17.8 + - - +
303A GLY* 3.6 6.3 - - - +
305A LEU* 1.3 76.1 - - - +
307A HIS* 1.3 62.2 + - - +
309A ILE* 3.4 1.1 + - - +
310A TYR* 3.1 29.6 + - - -
302D LEU* 4.3 1.9 - - + +
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Residues in contact with HIS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ALA* 3.7 10.2 + - + +
286A LEU* 3.7 25.2 - - + +
287A GLY* 3.3 33.4 - - - -
290A GLN* 2.8 26.1 + - + +
303A GLY 3.0 12.3 + - - +
304A SER 3.2 9.4 - - - +
306A ALA* 1.3 76.9 - - - +
308A GLN* 1.3 69.1 + - - +
310A TYR* 3.5 1.7 + - - +
311A ARG* 2.9 39.5 + - + +
294C THR* 3.3 34.0 - - + +
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLN* 3.2 8.3 + - - -
304A SER 3.0 14.1 + - - +
305A LEU* 3.2 0.4 + - - -
307A HIS* 1.3 105.7 + - - +
309A ILE* 1.3 59.1 + - - +
311A ARG* 3.3 8.0 - - - +
312A MET* 2.9 34.6 + - - +
290C GLN* 3.7 5.9 - - - +
293C ALA* 5.6 0.4 - - - +
298C SER 3.7 5.0 - - - +
299C PRO* 3.4 9.5 - - + +
300C ILE* 3.0 34.3 + - - +
301C LEU* 3.4 29.4 - - + +
304C SER* 3.1 27.1 + - - +
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ILE* 4.2 27.6 - - + -
305A LEU* 2.9 26.7 + - + +
306A ALA 3.7 3.6 - - - +
308A GLN* 1.3 75.7 - - - +
310A TYR* 1.3 57.7 + - + +
312A MET* 3.2 18.7 + - + +
313A MET* 3.0 32.0 + - - +
326A VAL* 4.1 25.6 - - + -
329A PHE* 4.3 11.3 - - + -
330A LEU* 6.0 2.0 - - + -
301C LEU* 4.4 6.1 - - + -
301D LEU* 3.7 41.5 - - + -
302D LEU* 4.6 5.4 - - + -
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Residues in contact with TYR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ALA* 4.2 9.4 - - + -
220A MET* 3.7 6.4 - - - +
221A ILE* 3.6 23.1 - - + -
279A THR* 3.8 18.8 - - + +
282A MET* 3.9 20.9 - - + -
283A ALA* 4.2 16.4 - - + -
286A LEU* 3.7 16.8 - - + -
306A ALA 3.1 26.5 + - - +
307A HIS 4.0 2.7 - - - +
309A ILE* 1.3 73.2 - - + +
311A ARG* 1.3 64.5 + - - +
313A MET* 3.4 19.4 + - + +
314A CYS* 3.1 27.0 + - - -
323A PHE* 2.8 53.6 + + + -
326A VAL* 3.7 17.3 - - + +
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Residues in contact with ARG 311 (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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280A THR* 5.7 4.0 + - - +
283A ALA* 3.7 26.3 + - - +
284A LYS* 5.0 1.8 - - - +
307A HIS* 2.9 27.1 + - + +
308A GLN* 3.3 16.6 - - - +
309A ILE 3.3 0.2 - - - -
310A TYR* 1.3 76.1 - - - +
312A MET* 1.3 63.6 + - - +
314A CYS* 3.3 39.5 + - - +
315A ALA* 3.4 12.1 + - - +
332B GLU* 5.5 4.8 + - - -
294C THR* 5.5 2.4 + - - +
297C LYS* 3.5 71.6 + - - +
298C SER 4.4 1.3 - - - +
299C PRO* 4.0 22.0 - - + -
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLN 2.9 14.5 + - - +
309A ILE* 3.2 25.5 + - + +
311A ARG* 1.3 73.9 - - - +
313A MET* 1.3 62.1 + - - +
315A ALA* 3.1 15.0 + - - +
316A LYS* 3.2 31.6 - - - +
329A PHE* 4.3 15.5 - - + -
312B MET* 3.9 21.3 - - + -
329B PHE* 4.3 17.5 - - - -
330B LEU* 4.2 15.7 - - + +
299C PRO* 3.9 20.6 - - + -
301C LEU* 3.6 31.9 - - + -
301D LEU* 5.3 0.2 - - + -
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Residues in contact with MET 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A THR* 3.8 14.4 - - + +
309A ILE* 3.0 17.2 + - - +
310A TYR* 3.5 37.0 - - + +
312A MET* 1.3 76.7 - - - +
314A CYS* 1.3 60.9 + - - +
316A LYS* 3.0 12.3 + - - -
317A GLY 3.4 0.5 + - - -
318A TYR* 3.1 37.2 + - + +
323A PHE 4.2 0.2 - - - +
325A SER* 3.5 25.6 - - - +
326A VAL* 3.6 39.7 - - - +
329A PHE* 3.6 26.2 - - + -
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Residues in contact with CYS 314 (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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279A THR* 3.8 6.5 - - - +
280A THR* 3.7 25.8 - - - -
283A ALA* 3.6 23.8 - - - -
310A TYR 3.1 19.8 + - - -
311A ARG* 3.5 28.7 - - - +
313A MET* 1.3 74.5 - - - +
315A ALA* 1.3 58.8 + - - +
316A LYS 3.2 0.8 + - - -
317A GLY* 4.2 4.3 + - - -
319A SER* 4.0 25.0 - - - +
332B GLU* 4.4 5.1 - - - +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ARG* 3.4 7.7 + - - +
312A MET* 3.1 11.4 + - - +
314A CYS* 1.3 78.3 - - + +
316A LYS* 1.3 66.2 + - + +
317A GLY 3.7 1.1 - - - -
330B LEU 5.5 3.8 - - - +
331B ARG 5.4 2.4 - - - +
332B GLU* 3.5 48.0 - - + +
299C PRO* 6.4 2.2 - - + -
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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
------------------------------------------------------------
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