Contacts of the helix formed by residues 305 - 319 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ARG* 3.6 31.4 - - + +
192B PHE 5.1 0.6 + - - -
302B PRO* 4.2 4.9 - - + -
303B LYS 2.9 0.2 - - - -
304B SER* 1.3 79.6 + - - +
306B ILE* 1.3 64.8 + - - +
307B GLY 3.1 3.4 - - - -
308B ARG* 2.9 22.1 + - + +
309B HIS* 3.3 24.4 + + + -
343C PTR 2.8 51.7 + + - -
13F C 4.3 9.6 - - - -
24G T 3.4 41.8 - - - -
25G A 3.2 13.6 + - - +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 3.8 29.8 - - + -
147B LEU* 4.7 12.1 - - + -
161B ILE* 4.6 2.5 - - + -
182B PHE* 3.7 25.4 - - + -
283B TYR* 4.9 0.4 - - - +
287B LEU* 4.4 4.3 - - + -
295B ILE* 4.8 4.0 - - + -
296B PHE* 3.6 34.1 - - + -
302B PRO* 4.0 12.3 - - + +
303B LYS 2.9 23.3 + - - +
304B SER 4.5 2.2 - - - +
305B HIS* 1.3 76.2 - - - +
307B GLY* 1.3 75.5 + - - +
309B HIS* 3.0 9.4 + - + +
310B LEU* 2.9 37.0 + - + +
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Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PHE* 4.4 9.2 - - - -
185B THR* 3.7 26.7 + - - -
186B PHE* 3.8 15.2 - - - -
304B SER 3.8 3.0 + - - -
305B HIS 3.0 1.6 + - - -
306B ILE* 1.3 86.5 - - - +
308B ARG* 1.3 60.7 + - - +
310B LEU* 3.3 7.2 + - - +
311B MET* 3.2 19.8 + - - +
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Residues in contact with ARG 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B THR 4.5 1.6 + - - -
189B CYS* 3.6 31.4 + - - +
190B GLY 4.2 12.1 + - - +
191B ARG* 3.7 36.0 - - - +
194B ASP* 5.0 2.2 + - - -
304B SER 4.9 0.6 + - - -
305B HIS* 2.9 26.6 + - + +
307B GLY* 1.3 73.9 - - - +
309B HIS* 1.3 58.0 + - - +
311B MET 4.1 0.2 - - - -
312B THR* 2.6 35.3 + - - +
328B GLY* 2.4 34.4 + - - -
329B ASN 4.0 2.2 + - - -
330B TRP* 2.5 40.6 - - - -
343C PTR 2.5 44.6 + - + -
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Residues in contact with HIS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 4.6 11.9 - - + +
302B PRO* 3.7 26.4 - - + +
305B HIS* 3.3 30.1 + + - -
306B ILE* 3.0 8.5 + - + +
308B ARG* 1.3 75.0 - - - +
310B LEU* 1.3 68.6 + - + +
312B THR* 3.2 2.7 + - - -
313B SER* 2.8 28.7 + - - -
342C THR 3.5 7.7 + - - -
343C PTR 3.4 46.3 - + - +
345C HIS* 3.0 37.6 + + + -
13F C 4.6 12.1 + - - -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 4.1 15.9 - - + -
148B LEU* 4.0 25.8 - - + -
154B ILE* 4.1 15.6 - - + +
157B ILE* 4.5 9.4 - - + -
158B THR* 4.7 8.1 - - - +
161B ILE* 4.3 7.6 - - + -
182B PHE* 4.0 28.0 - - + -
186B PHE* 4.0 17.0 - - + -
306B ILE* 2.9 32.7 + - + +
307B GLY* 3.3 8.3 + - - +
309B HIS* 1.3 77.3 - - + +
311B MET* 1.3 51.2 + - - +
313B SER* 3.1 6.9 + - - -
314B PHE* 2.6 34.3 + - - +
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Residues in contact with MET 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PHE* 3.3 57.7 - - + +
187B ILE 4.3 0.2 - - - +
189B CYS* 3.6 28.9 - - + -
307B GLY 3.2 8.9 + - - +
308B ARG 4.4 0.2 - - - +
310B LEU* 1.3 75.0 - - - +
312B THR* 1.3 61.3 + - - +
314B PHE* 3.4 24.0 - - + +
315B LEU* 2.8 44.1 + - + +
354B TYR* 3.4 24.5 - - - +
358B VAL* 4.1 18.2 - - + -
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Residues in contact with THR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B CYS* 3.8 7.2 - - - -
308B ARG 2.6 22.0 + - - -
309B HIS 3.2 4.6 + - - -
311B MET* 1.3 78.4 - - - +
313B SER* 1.3 62.9 + - - +
315B LEU* 3.5 8.1 + - - +
316B SER* 3.1 21.7 + - - -
324B THR* 4.4 20.1 + - + +
330B TRP* 3.7 21.0 - - + -
339C ALA 4.1 4.5 - - - +
343C PTR 3.7 24.6 - - + +
344C THR* 3.5 21.1 - - - +
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.2 31.9 - - - +
154B ILE* 4.8 0.7 - - - -
309B HIS 2.8 20.3 + - - -
310B LEU* 3.3 8.3 - - - -
312B THR* 1.3 75.0 - - - +
314B PHE* 1.3 66.8 + - - +
316B SER* 3.2 5.9 + - - -
317B MET* 2.8 29.1 + - - +
343C PTR 3.4 2.9 + - - -
344C THR* 4.8 0.2 - - - +
345C HIS* 3.3 28.9 + - - +
346C GLN* 4.5 5.1 + - - +
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 4.2 34.3 - - + +
155B TRP* 4.9 22.7 - + - -
186B PHE* 5.1 2.9 - + - -
310B LEU 2.6 17.9 + - - +
311B MET* 3.4 35.7 - - + +
313B SER* 1.3 73.4 - - - +
315B LEU* 1.3 63.7 + - + +
317B MET* 3.7 7.9 - - - +
318B LYS* 2.8 59.2 + - + +
357B LEU* 3.5 39.9 - - + -
358B VAL* 4.7 10.8 - - + -
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B CYS* 5.6 1.8 - - - -
311B MET* 2.8 33.2 + - + +
312B THR* 3.7 6.3 - - - +
314B PHE* 1.3 86.7 - - + +
316B SER* 1.3 60.7 + - - +
318B LYS* 3.5 3.1 + - - -
319B GLY 3.1 4.0 + - - -
320B LEU* 2.8 56.6 + - + +
323B LEU* 4.2 13.2 - - + -
324B THR* 3.8 37.0 - - + +
327B VAL* 4.2 19.5 - - + -
354B TYR* 4.2 13.5 - - + -
357B LEU* 5.5 1.3 - - + -
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Residues in contact with SER 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B THR 3.1 17.2 + - - -
313B SER* 3.6 3.8 - - - -
315B LEU* 1.3 75.8 - - - +
317B MET* 1.3 56.1 + - - +
319B GLY* 2.7 22.9 + - - -
321B THR* 3.8 20.0 - - - +
324B THR* 4.9 0.6 + - - -
344C THR* 3.6 30.6 - - - +
346C GLN 3.7 5.9 + - - -
348C THR* 3.2 32.8 + - - +
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Residues in contact with MET 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 5.8 2.9 - - - -
313B SER 2.8 17.0 + - - +
314B PHE* 3.7 9.6 - - - +
316B SER* 1.3 73.8 - - - +
318B LYS* 1.3 91.2 + - + +
319B GLY 3.4 0.3 + - - -
346C GLN* 3.0 49.5 + - + +
347C ILE 4.5 4.0 - - - +
348C THR* 4.4 9.9 - - - +
349C ALA* 3.8 27.1 + - + +
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Residues in contact with LYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B PHE* 2.8 54.6 + - + +
315B LEU* 4.0 3.8 - - - +
317B MET* 1.3 94.3 - - + +
319B GLY* 1.3 62.1 + - - +
320B LEU* 4.5 12.8 - - + -
357B LEU* 4.6 16.2 - - + +
363B ALA* 6.0 2.0 - - - +
364B TYR* 4.1 33.1 + - + +
366B PRO* 5.2 4.7 - - - +
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Residues in contact with GLY 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B LEU 3.1 0.2 + - - -
316B SER 2.7 15.7 + - - -
317B MET 3.2 0.8 - - - -
318B LYS* 1.3 81.4 - - - +
320B LEU* 1.3 65.9 + - - +
321B THR* 3.7 3.6 - - - -
322B GLU* 5.4 0.7 - - - +
364B TYR* 4.1 9.0 + - - -
334C ARG* 4.9 10.0 + - - -
348C THR* 4.5 10.5 - - - -
349C ALA 6.0 1.1 - - - -
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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
------------------------------------------------------------
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