Contacts of the helix formed by residues 305 - 319 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191D ARG* 3.9 23.3 - - + +
192D PHE 5.1 0.2 + - - -
302D PRO* 4.3 5.2 - - + -
303D LYS 2.8 0.4 + - - -
304D SER* 1.3 77.1 + - - +
306D ILE* 1.3 64.1 + - - +
307D GLY 3.1 2.7 - - - -
308D ARG* 2.9 31.3 + - + +
309D HIS* 2.9 39.8 + + + -
13H C 4.4 12.5 + - - -
14H T 3.2 29.2 + - - -
24J T 3.4 42.9 + - - +
25J A 3.0 13.8 + - - +
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Residues in contact with ILE 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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144D LEU* 4.8 10.3 - - + -
147D LEU* 4.8 15.5 - - + -
161D ILE* 4.4 2.2 - - + -
182D PHE* 3.8 22.9 - - + -
283D TYR* 4.8 0.4 - - - +
287D LEU* 4.3 5.8 - - + -
295D ILE* 5.0 6.5 - - + -
296D PHE* 3.5 37.9 - - + -
302D PRO* 4.2 19.0 - - + +
303D LYS 2.7 25.2 + - - +
304D SER 4.2 2.5 - - - +
305D HIS* 1.3 70.7 - - - +
307D GLY* 1.3 74.6 + - - +
309D HIS* 3.1 11.9 + - + +
310D LEU* 2.9 42.4 + - + +
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Residues in contact with GLY 307 (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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182D PHE* 4.2 11.4 - - - -
185D THR* 3.5 20.4 - - - -
186D PHE* 3.6 20.5 - - - -
304D SER 3.6 3.2 + - - -
305D HIS 3.1 1.2 - - - -
306D ILE* 1.3 88.0 - - - +
308D ARG* 1.3 64.5 + - - +
310D LEU* 3.3 6.0 + - - +
311D MET* 3.3 15.4 + - - +
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Residues in contact with ARG 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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185D THR* 4.3 3.2 + - - -
189D CYS* 3.3 39.8 + - - +
190D GLY* 3.6 19.3 + - - +
191D ARG* 3.7 41.3 - - - +
194D ASP* 4.6 0.4 + - - -
304D SER 4.7 0.6 + - - -
305D HIS* 2.9 26.6 + - + +
307D GLY* 1.3 77.2 - - - +
309D HIS* 1.3 65.1 + - + +
311D MET* 3.2 3.3 + - - +
312D THR* 3.1 23.0 + - - -
328D GLY 3.2 22.6 + - - -
329D ASN 4.3 1.6 + - - -
330D TRP* 3.3 35.8 - - + +
14H T 3.0 30.3 + - - -
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Residues in contact with HIS 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TYR* 2.9 61.6 - + + +
144D LEU* 4.1 15.5 - - + -
302D PRO* 4.0 13.8 - - + +
305D HIS* 2.9 51.6 + + + -
306D ILE* 3.6 11.6 + - + +
308D ARG* 1.3 76.9 - - + +
310D LEU* 1.3 62.4 + - - +
312D THR* 3.2 9.4 + - - -
313D SER* 2.7 29.8 + - - -
13H C 5.0 4.7 + - - -
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 4.9 2.0 - - + -
147D LEU* 4.8 7.6 - - + -
148D LEU* 4.2 11.2 - - + -
154D ILE* 3.9 24.5 - - + +
157D ILE* 4.2 20.4 - - + -
158D THR* 4.6 8.3 - - - +
161D ILE* 4.0 7.4 - - + -
182D PHE* 3.7 34.5 - - + -
186D PHE* 3.7 13.7 - - + -
306D ILE* 2.9 31.3 + - + +
307D GLY* 3.5 7.2 - - - +
309D HIS* 1.3 77.6 - - - +
311D MET* 1.3 57.1 + - - +
313D SER* 3.2 7.0 + - - -
314D PHE* 2.7 28.2 + - - +
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Residues in contact with MET 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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186D PHE* 3.3 69.1 - - + +
187D ILE 4.2 0.2 - - - +
189D CYS* 3.9 16.8 - - + -
307D GLY 3.3 3.4 + - - +
308D ARG 3.2 7.6 + - - +
310D LEU* 1.3 76.4 - - - +
312D THR* 1.3 65.7 + - - +
314D PHE* 3.6 22.9 - - + -
315D LEU* 3.0 37.1 + - + +
354D TYR* 3.4 23.8 - - + +
358D VAL* 3.8 23.1 - - + -
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Residues in contact with THR 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TYR 5.2 12.1 - - - +
189D CYS* 3.8 13.7 - - - -
308D ARG 3.1 15.7 + - - -
309D HIS* 3.5 12.4 - - - -
311D MET* 1.3 77.4 - - - +
313D SER* 1.3 62.7 + - - +
315D LEU* 3.7 3.3 + - - +
316D SER* 3.2 22.7 + - - -
324D THR* 4.1 25.4 + - + +
330D TRP* 4.1 12.6 - - + -
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Residues in contact with SER 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TYR* 5.8 1.7 + - - +
144D LEU* 4.6 6.9 - - - +
148D LEU* 3.8 23.9 - - - +
154D ILE* 4.0 15.0 - - - -
309D HIS 2.7 19.5 + - - -
310D LEU* 3.4 8.0 - - - -
312D THR* 1.3 75.5 - - - +
314D PHE* 1.3 58.2 + - - +
316D SER* 3.0 6.1 + - - -
317D MET* 2.7 38.7 + - - +
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Residues in contact with PHE 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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154D ILE* 3.8 36.0 - - + +
155D TRP* 3.9 31.4 - + - -
186D PHE* 4.5 2.2 - + + -
310D LEU 2.7 20.0 + - - +
311D MET* 3.3 30.5 + - + +
313D SER* 1.3 73.2 - - - +
315D LEU* 1.3 55.9 + - + +
317D MET* 3.7 6.8 - - - +
318D LYS* 2.8 68.5 + - + +
357D LEU* 3.7 33.7 - - + -
358D VAL* 4.4 12.6 - - + -
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Residues in contact with LEU 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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189D CYS* 5.9 1.6 - - + -
311D MET* 3.0 29.9 + - + +
312D THR* 3.9 1.8 - - - +
314D PHE* 1.3 88.9 - - + +
316D SER* 1.3 58.2 + - - +
318D LYS* 3.4 3.5 + - - -
319D GLY 3.0 5.2 + - - -
320D LEU* 2.7 54.3 + - + +
323D LEU* 4.5 5.2 - - + -
324D THR* 3.8 40.2 - - + +
327D VAL* 4.5 7.6 - - + -
354D TYR* 4.0 35.0 - - + -
357D LEU* 4.7 9.6 - - + -
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Residues in contact with SER 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D THR* 3.2 13.6 + - - -
313D SER* 3.0 11.1 + - - -
315D LEU* 1.3 75.6 - - - +
317D MET* 1.3 58.9 + - - +
319D GLY* 2.5 28.8 + - - -
321D THR* 3.5 28.6 - - - +
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Residues in contact with MET 317 (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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153D SER* 6.4 2.0 - - - -
154D ILE* 5.3 9.0 - - + -
313D SER* 2.7 21.8 + - - +
314D PHE* 3.8 10.3 - - - +
316D SER* 1.3 74.5 + - - +
318D LYS* 1.3 92.0 + - + +
319D GLY* 3.3 0.9 + - - -
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Residues in contact with LYS 318 (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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314D PHE* 2.8 56.4 + - + +
315D LEU 3.9 4.0 - - - +
317D MET* 1.3 92.0 - - + +
319D GLY* 1.3 59.9 + - - +
320D LEU* 4.8 2.7 - - + -
357D LEU* 4.5 27.0 - - + +
363D ALA* 5.3 6.9 - - - +
364D TYR* 3.6 32.8 + - + +
366D PRO* 5.1 5.0 - - - +
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Residues in contact with GLY 319 (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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315D LEU 3.0 0.2 + - - -
316D SER 2.5 21.8 + - - -
317D MET 3.1 1.4 - - - -
318D LYS* 1.3 73.5 - - - +
320D LEU* 1.3 66.9 + - - +
321D THR* 3.8 3.4 - - - -
322D GLU* 5.5 0.9 - - - +
364D TYR* 3.6 16.0 + - - -
366D PRO* 6.3 0.4 - - - -
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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