Contacts of the helix formed by residues 305 - 318 (chain A) in PDB entry 1M6X
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 HIS 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ARG* 3.8 30.4 - - + +
192A PHE 4.7 0.6 + - - -
302A PRO* 4.4 4.5 - - + -
303A LYS 3.0 0.4 - - - -
304A SER* 1.3 80.7 + - - +
306A ILE* 1.3 53.2 + - - +
307A GLY 3.0 3.1 - - - -
308A ARG* 2.6 45.8 + - + +
309A HIS* 3.4 16.6 + + + -
343D PTR 3.2 48.4 + + - -
13E C 4.5 8.8 - - - -
24H T 3.0 45.2 - - - -
25H A 3.5 11.6 + - - +
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Residues in contact with ILE 306 (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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144A LEU* 4.0 26.5 - - + -
147A LEU* 4.4 15.5 - - + -
161A ILE* 4.4 2.9 - - + -
182A PHE* 3.6 25.1 - - + -
283A TYR* 4.8 0.2 - - - +
287A LEU* 4.4 3.1 - - + -
295A ILE* 5.0 3.4 - - + -
296A PHE* 3.6 34.5 - - + -
302A PRO* 4.3 7.4 - - + +
303A LYS* 2.9 27.2 + - - +
304A SER 4.2 1.3 - - - +
305A HIS* 1.3 76.1 - - - +
307A GLY* 1.3 74.2 + - - +
309A HIS* 3.2 12.4 + - + +
310A LEU* 2.9 37.0 + - + +
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Residues in contact with GLY 307 (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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182A PHE* 4.2 9.6 - - - -
185A THR* 3.6 19.9 + - - -
186A PHE* 3.6 22.7 - - - -
304A SER 3.7 2.2 + - - -
305A HIS 2.7 6.1 + - - -
306A ILE* 1.3 84.4 - - - +
308A ARG* 1.3 60.1 + - - -
310A LEU* 3.4 7.0 + - - +
311A MET* 3.2 17.8 + - - +
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Residues in contact with ARG 308 (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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185A THR* 4.3 2.8 + - - -
189A CYS* 3.3 33.7 + - - +
190A GLY 4.1 17.5 + - - +
191A ARG* 3.9 35.3 - - - +
194A ASP* 5.1 1.4 + - - -
305A HIS* 2.6 25.8 + - - +
307A GLY* 1.3 70.7 - - - -
309A HIS* 1.3 62.5 + - - +
311A MET 3.3 2.3 + - - -
312A THR* 3.0 25.8 + - - +
328A GLY 2.5 33.5 + - - -
329A ASN 4.1 1.8 + - - -
330A TRP* 3.0 33.7 - - - -
343D PTR 2.4 50.1 + - + -
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Residues in contact with HIS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 4.9 8.8 - - + +
302A PRO* 3.8 25.9 - - + +
305A HIS* 3.6 24.3 + + + -
306A ILE* 3.2 14.6 + - + +
308A ARG* 1.3 78.5 - - - +
310A LEU* 1.3 61.9 + - + +
312A THR* 3.3 0.9 + - - -
313A SER* 2.8 30.3 + - - -
342D THR 3.3 12.6 + - - -
343D PTR 3.2 47.6 - + - +
345D HIS* 3.2 31.8 - + + +
13E C 4.5 11.7 + - - -
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Residues in contact with LEU 310 (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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147A LEU* 4.3 13.2 - - + -
148A LEU* 4.2 15.3 - - + -
154A ILE* 3.9 28.4 - - + +
157A ILE* 4.5 10.1 - - + -
158A THR* 4.6 8.1 - - - +
161A ILE* 4.3 6.7 - - + -
182A PHE* 3.9 29.2 - - + -
186A PHE* 3.7 17.0 - - + -
306A ILE* 2.9 33.0 + - + +
307A GLY* 3.6 7.9 - - - +
308A ARG 3.2 0.2 - - - -
309A HIS* 1.3 76.5 - - + +
311A MET* 1.3 51.0 + - - +
313A SER* 3.2 6.7 + - - -
314A PHE* 2.7 34.3 + - - +
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Residues in contact with MET 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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186A PHE* 3.3 54.9 - - + +
187A ILE 4.0 0.9 - - - +
189A CYS* 3.5 27.8 - - + -
307A GLY 3.2 5.8 + - - +
308A ARG 3.3 2.2 + - - +
310A LEU* 1.3 75.7 - - - +
312A THR* 1.3 60.9 + - - +
314A PHE* 3.5 22.7 - - + -
315A LEU* 2.9 43.9 + - + +
327A VAL* 4.6 0.2 - - + -
354A TYR* 3.0 28.3 - - - +
358A VAL* 3.8 22.2 - - + -
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Residues in contact with THR 312 (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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189A CYS* 3.6 6.0 - - - -
308A ARG 3.0 15.8 + - - -
309A HIS 3.5 3.4 - - - -
311A MET* 1.3 75.6 - - - +
313A SER* 1.3 57.3 + - - +
315A LEU* 3.6 8.4 + - - +
316A SER* 3.1 26.3 + - - -
324A THR* 4.5 9.9 + - + -
330A TRP* 3.5 21.5 - - + -
339D ALA* 3.5 23.8 - - + +
343D PTR 3.5 39.0 - - + +
344D THR* 3.7 5.4 - - - +
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Residues in contact with SER 313 (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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148A LEU* 3.6 27.9 - - - +
154A ILE* 4.7 3.4 - - - -
309A HIS 2.8 18.7 + - - -
310A LEU* 3.5 5.6 - - - -
312A THR* 1.3 74.8 - - - +
314A PHE* 1.3 57.6 - - - +
316A SER* 3.1 6.1 + - - -
317A MET* 2.7 38.5 + - - +
343D PTR 3.1 12.1 + - - -
344D THR* 4.8 4.0 - - - +
345D HIS* 3.6 15.5 + - - -
346D GLN* 5.6 2.5 - - - -
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Residues in contact with PHE 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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154A ILE* 4.4 31.1 - - + +
155A TRP* 4.7 22.7 - + - -
186A PHE* 4.7 4.3 - + + -
310A LEU 2.7 21.1 + - - +
311A MET* 3.5 30.5 - - + +
313A SER* 1.3 72.3 - - - +
315A LEU* 1.3 62.8 + - + +
317A MET* 3.8 7.8 - - - +
318A LYS* 2.8 58.5 + - + +
357A LEU* 3.3 44.6 - - + -
358A VAL* 4.3 14.8 - - + -
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Residues in contact with LEU 315 (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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189A CYS* 5.6 2.2 - - - -
311A MET* 2.9 33.4 + - + +
312A THR* 3.8 3.4 - - - +
314A PHE* 1.3 87.1 - - + +
316A SER* 1.3 62.1 + - - +
318A LYS* 3.3 3.3 + - - -
319A GLY 3.2 3.3 + - - -
320A LEU* 2.9 54.5 + - + +
323A LEU* 4.3 6.7 - - + -
324A THR* 3.7 40.2 - - + +
327A VAL* 4.2 18.2 - - + -
354A TYR* 3.9 23.3 - - + -
357A LEU* 5.3 1.6 - - + -
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Residues in contact with SER 316 (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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312A THR 3.1 18.0 + - - -
313A SER* 3.6 4.0 - - - -
315A LEU* 1.3 75.4 - - - +
317A MET* 1.3 55.9 + - - +
319A GLY* 2.7 27.4 + - - -
321A THR* 3.7 25.9 - - - +
324A THR* 4.9 0.6 + - - -
344D THR* 3.9 27.9 - - - +
346D GLN 5.0 2.3 + - - -
348D THR* 4.4 24.3 + - - +
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Residues in contact with MET 317 (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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154A ILE* 5.6 7.4 - - + -
313A SER 2.7 21.7 + - - +
314A PHE* 3.9 10.5 - - - +
316A SER* 1.3 75.3 + - - +
318A LYS* 1.3 92.7 + - + +
319A GLY* 3.2 1.4 + - - -
346D GLN* 4.2 27.4 - - + +
348D THR* 5.8 5.5 - - - +
349D ALA* 5.4 10.5 + - - +
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Residues in contact with LYS 318 (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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314A PHE* 2.8 53.6 + - + +
315A LEU* 3.8 5.2 - - - +
316A SER 3.0 0.4 + - - -
317A MET* 1.3 96.2 - - + +
319A GLY* 1.3 62.8 + - - +
320A LEU* 4.1 13.0 - - + +
357A LEU* 4.2 14.9 - - + +
363A ALA* 5.4 4.2 - - - +
364A TYR* 3.6 47.2 + - + +
366A PRO* 5.3 3.5 - - - +
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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