Contacts of the helix formed by residues 302 - 315 (chain M) in PDB entry 4G7H
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 VAL 302 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146M VAL* 4.4 9.9 - - + -
162M ILE* 4.3 9.6 - - + -
269M LEU* 5.0 7.4 - - + -
277M ALA* 5.7 2.9 - - + -
281M LEU* 4.6 4.0 - - + +
283M ILE* 4.9 3.1 - - - -
285M LEU* 3.9 26.0 - - + -
289M THR 4.0 0.7 - - - +
290M LEU* 3.0 49.8 + - + +
301M GLU* 1.3 81.3 - - - +
303M PHE* 1.3 64.7 + - + +
304M LEU 3.4 1.6 - - - -
305M PRO* 3.0 15.0 - - - +
306M THR* 3.3 30.7 + - + +
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Residues in contact with PHE 303 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162M ILE* 4.6 14.6 - - + -
172M ILE* 4.7 3.6 - - + -
174M LEU* 4.9 6.0 - - + +
184M MET* 3.7 20.9 - - + -
193M LEU* 4.5 11.7 - - + +
196M LEU* 3.6 31.4 - - + -
197M LEU* 4.7 11.2 - - + -
200M LEU* 4.0 14.1 - - + -
261M ILE* 3.9 21.3 - - + -
290M LEU* 3.7 45.5 - - + -
291M ALA* 5.0 0.7 - - + -
300M ASP* 3.3 23.3 + - - +
302M VAL* 1.3 76.4 - - + +
304M LEU* 1.3 58.9 + - - +
306M THR* 2.9 20.7 + - - -
307M LEU* 2.9 18.2 + - - +
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Residues in contact with LEU 304 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197M LEU* 5.0 5.1 - - + +
202M TYR* 3.2 44.6 - - + +
207M LEU* 4.2 22.2 - - + -
210M GLU* 4.5 28.3 - - + +
211M LEU* 4.4 22.4 - - + -
300M ASP* 3.0 12.2 + - - +
303M PHE* 1.3 73.7 - - - +
305M PRO* 1.4 65.0 - - + +
307M LEU* 3.7 9.1 - - + +
308M ARG* 2.9 33.6 + - + +
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Residues in contact with PRO 305 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281M LEU* 3.9 14.5 - - + +
283M ILE* 3.7 45.3 - - + -
300M ASP* 4.3 0.7 - - - +
301M GLU 3.8 8.3 - - - +
302M VAL 3.0 20.9 - - - +
304M LEU* 1.4 89.4 - - + +
306M THR* 1.3 55.5 - - - +
308M ARG* 3.5 13.7 + - + +
309M TYR* 2.9 28.8 + - - +
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Residues in contact with THR 306 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146M VAL* 3.8 22.4 - - + -
148M PHE* 3.7 7.7 - - - -
160M ALA* 4.9 2.0 - - - +
162M ILE* 4.2 8.1 - - + +
174M LEU* 3.8 16.6 - - - +
281M LEU* 3.5 24.0 - - + -
302M VAL* 3.3 33.1 + - + +
303M PHE* 2.9 20.6 + - - -
305M PRO* 1.3 73.3 - - - +
307M LEU* 1.3 60.0 + - - +
309M TYR* 3.4 0.6 + - - -
310M LEU* 2.9 28.9 + - - +
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Residues in contact with LEU 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174M LEU* 4.7 5.2 - - + -
182M VAL* 4.1 8.7 - - + -
193M LEU* 3.7 29.6 - - + -
197M LEU* 3.9 11.4 - - + -
207M LEU* 5.8 0.7 - - + -
211M LEU* 3.7 18.6 - - + -
221M LEU* 3.6 26.0 - - + -
303M PHE 2.9 14.5 + - - +
304M LEU* 3.7 11.2 - - + +
306M THR* 1.3 77.9 + - - +
308M ARG* 1.3 59.8 + - - +
310M LEU* 3.3 14.2 + - + +
311M PHE* 2.9 53.4 + - + +
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Residues in contact with ARG 308 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210M GLU* 5.2 10.1 - - + +
211M LEU* 4.3 20.8 - - + +
214M TYR* 3.2 32.6 + - + +
281M LEU 3.5 23.8 + - - -
304M LEU* 2.9 21.6 + - + +
305M PRO* 3.6 14.4 + - + +
307M LEU* 1.3 78.5 - - - +
309M TYR* 1.3 78.6 + - - +
311M PHE* 3.5 3.0 + - - +
312M ALA* 2.9 30.3 + - - +
320M HIS* 2.9 34.8 + - - -
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Residues in contact with TYR 309 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148M PHE* 3.4 42.6 - + + -
280M LYS* 3.0 51.9 + - - +
281M LEU* 4.1 7.9 - - + -
305M PRO 2.9 18.7 + - - +
306M THR 3.7 0.2 - - - +
307M LEU 3.3 0.2 - - - -
308M ARG* 1.3 92.8 - - - +
310M LEU* 1.3 61.2 + - - +
312M ALA* 3.4 2.1 + - - +
313M LEU* 2.9 29.9 + - + +
319M GLY 4.1 5.3 + - - -
320M HIS* 3.5 32.6 - + + -
321M GLU* 3.1 24.2 + - - +
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Residues in contact with LEU 310 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148M PHE* 3.8 14.3 - - + -
158M TYR* 4.0 32.1 - - + +
160M ALA* 4.3 9.9 - - + +
174M LEU* 3.9 35.2 - - + +
175M GLU* 4.6 1.3 - - - +
176M VAL* 4.3 24.0 - - + +
182M VAL* 5.8 1.8 - - + -
306M THR 2.9 17.7 + - - +
307M LEU* 3.5 17.3 - - + +
309M TYR* 1.3 77.7 - - - +
311M PHE* 1.3 59.6 + - + +
313M LEU* 3.2 3.7 + - + +
314M THR* 2.9 41.1 + - - +
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Residues in contact with PHE 311 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176M VAL* 3.7 30.5 - - + -
182M VAL* 3.4 24.9 - - + -
211M LEU* 3.4 46.7 - - + -
214M TYR* 4.1 11.8 - - + -
217M LEU* 3.5 49.4 - - + +
218M VAL* 4.3 0.9 - - + -
221M LEU* 4.7 8.1 - - + -
307M LEU* 2.9 29.3 + - + +
308M ARG* 3.9 3.8 - - - +
310M LEU* 1.3 77.9 - - + +
312M ALA* 1.3 58.0 + - - +
314M THR* 3.2 6.1 + - - -
315M ALA* 2.9 33.0 + - - +
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Residues in contact with ALA 312 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214M TYR* 3.3 40.3 - - + +
308M ARG* 2.9 14.7 + - - +
309M TYR 3.7 0.2 - - - +
310M LEU 3.3 0.2 - - - -
311M PHE* 1.3 76.0 - - - +
313M LEU* 1.3 58.8 + - - +
316M GLY 3.3 2.4 + - - -
317M VAL* 2.9 33.1 + - + +
320M HIS* 3.3 32.8 - - + +
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Residues in contact with LEU 313 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148M PHE* 3.8 30.7 - - + -
158M TYR* 3.7 52.2 + - + +
309M TYR* 2.9 19.3 + - + +
310M LEU* 3.5 4.9 - - - +
311M PHE 3.1 0.2 - - - -
312M ALA* 1.3 75.8 - - - +
314M THR* 1.3 64.3 + - - +
316M GLY* 2.9 15.1 + - - -
317M VAL 4.9 0.7 - - - +
320M HIS* 3.5 38.1 - - + +
321M GLU* 4.1 10.3 - - - +
322M VAL* 4.1 7.0 - - + +
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Residues in contact with THR 314 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M GLY 3.8 19.6 - - - +
157M ARG* 4.1 23.8 - - - +
158M TYR* 3.8 22.9 + - - +
176M VAL* 4.9 7.3 - - + +
217M LEU* 5.2 12.8 - - + -
310M LEU* 2.9 26.6 + - - +
311M PHE* 3.8 8.9 - - + -
313M LEU* 1.3 76.3 - - - +
315M ALA* 1.3 61.0 + - - +
316M GLY* 3.3 1.4 + - - -
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Residues in contact with ALA 315 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214M TYR* 4.3 17.9 - - + -
215M GLY 4.7 7.0 - - - +
217M LEU* 4.8 8.9 - - + +
311M PHE 2.9 17.3 + - - +
312M ALA 4.0 4.5 - - - +
314M THR* 1.3 75.8 - - - +
316M GLY* 1.3 61.5 + - - +
317M VAL* 3.4 13.0 - - + +
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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
------------------------------------------------------------
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