Contacts of the helix formed by residues 250 - 265 (chain A) in PDB entry 3MQ6
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 LEU 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A LEU* 3.8 31.6 - - + -
246A ARG 3.5 16.4 - - - +
247A SER* 3.6 22.2 + - - +
248A ASP 3.3 3.0 - - - -
249A ARG* 1.3 79.9 - - - +
251A TYR* 1.3 66.2 + - + +
252A GLN 3.6 1.1 - - - -
253A PRO* 3.2 12.2 - - - +
254A LEU 3.9 0.9 + - - -
286A ASN* 6.2 0.7 - - + -
287A ALA* 3.7 35.7 - - + +
290A THR* 3.9 22.2 - - + +
291A TYR* 2.8 45.3 + - + +
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Residues in contact with TYR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A SER 3.2 25.7 + - - -
248A ASP 4.0 4.4 + - - +
249A ARG 3.5 2.2 - - - -
250A LEU* 1.3 81.4 - - + +
252A GLN* 1.3 60.8 + - - +
253A PRO 3.3 2.0 - - - -
254A LEU* 3.7 11.0 - - + -
255A TYR* 2.7 33.4 + - - +
290A THR* 4.0 31.5 + - + +
185B SER* 4.3 18.2 + - - -
251B TYR* 3.7 7.4 - - + +
252B GLN* 3.6 55.4 - - + +
255B TYR* 3.7 35.9 - + + -
256B GLU* 5.0 3.1 + - - -
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Residues in contact with GLN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER* 3.7 14.5 + - - +
186A THR 3.2 24.8 + - - +
187A PRO* 5.0 2.1 - - - +
240A ALA* 4.9 4.2 - - - +
242A LYS* 5.1 7.3 + - - +
249A ARG 5.1 0.6 + - - -
251A TYR* 1.3 75.1 - - - +
253A PRO* 1.3 84.4 - - + +
255A TYR* 4.0 0.9 - - - +
256A GLU* 2.9 36.2 + - + +
275A PHE* 5.8 0.2 - - - -
248B ASP* 4.4 17.2 + - + +
251B TYR* 3.6 42.9 - - + +
8K C 5.4 6.6 + - - +
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Residues in contact with PRO 253 (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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240A ALA* 3.7 25.8 - - + -
242A LYS* 3.5 28.0 - - + -
250A LEU 3.2 16.8 - - - +
252A GLN* 1.3 108.2 - - + +
254A LEU* 1.3 61.5 + - - +
257A ALA* 3.0 27.4 + - - +
275A PHE* 3.8 17.0 - - + -
277A VAL* 4.1 13.2 - - + -
291A TYR* 4.3 3.1 - - - +
310A ILE* 3.8 3.7 - - - +
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU 3.9 9.6 + - - +
251A TYR* 3.3 23.2 + - + +
253A PRO* 1.3 81.4 - - - +
255A TYR* 1.3 61.6 + - - +
257A ALA* 3.7 1.7 - - - +
258A ASN* 2.9 31.7 + - - +
290A THR* 4.4 14.6 - - + +
291A TYR* 4.2 9.8 - - + -
293A ALA* 4.3 18.8 - - + +
309A ALA* 3.6 24.5 - - + -
310A ILE* 3.8 18.1 - - + +
255B TYR* 3.4 39.3 - - + +
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Residues in contact with TYR 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 3.7 10.4 - - - +
183A PRO 5.1 6.8 + - - -
251A TYR 2.7 21.4 + - - +
252A GLN 4.0 2.0 - - - +
254A LEU* 1.3 73.9 - - - +
256A GLU* 1.3 71.4 + - - +
258A ASN* 3.2 9.0 + - + +
259A VAL* 3.0 44.0 + - + +
251B TYR* 3.8 33.2 - + + -
254B LEU* 3.7 24.5 - - + -
255B TYR* 4.5 21.0 - + + -
258B ASN* 3.6 26.2 + - - -
293B ALA* 3.7 21.9 - - + +
294B ALA 4.8 0.3 + - - -
296B LEU* 4.1 17.6 - - + +
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Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TRP* 3.0 24.6 + - + +
183A PRO 5.0 0.9 - - - +
184A THR* 3.5 7.6 - - - +
185A SER* 2.8 45.2 + - - +
186A THR 3.9 13.9 - - - +
187A PRO 4.7 2.0 - - - -
252A GLN* 2.9 29.2 + - - +
253A PRO* 4.1 3.4 - - + +
255A TYR* 1.3 89.4 - - - +
257A ALA* 1.3 52.7 + - - +
259A VAL* 3.2 7.1 + - - +
260A MET* 2.8 38.4 + - + +
275A PHE* 4.4 6.3 - - + -
251B TYR* 4.9 3.6 + - - -
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Residues in contact with ALA 257 (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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253A PRO 3.0 19.1 + - - +
254A LEU 3.7 4.3 - - - +
256A GLU* 1.3 72.7 - - - +
258A ASN* 1.3 61.1 + - - +
260A MET* 3.3 3.2 + - - +
261A GLN* 2.8 38.8 + - - +
275A PHE* 3.4 34.4 - - + -
309A ALA 3.6 21.1 - - - +
310A ILE* 3.8 4.9 - - + -
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Residues in contact with ASN 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 2.9 26.3 + - - +
255A TYR* 3.2 10.5 + - + +
257A ALA* 1.3 77.4 - - - +
259A VAL* 1.3 56.6 + - - +
261A GLN* 3.3 8.0 + - - +
262A LEU* 3.0 28.4 + - - +
294A ALA 5.0 1.4 + - - -
295A SER* 3.6 6.1 + - - -
296A LEU* 2.9 41.5 + - - +
297A TYR* 4.4 4.7 + - - +
309A ALA* 3.8 14.7 - - - +
255B TYR* 3.6 25.4 + - + -
296B LEU* 3.8 17.7 - - + +
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 4.3 17.7 - - + -
183A PRO 4.3 8.3 - - - +
184A THR* 3.6 29.6 - - + -
255A TYR* 3.0 53.9 + - + +
256A GLU* 3.6 13.2 - - - +
258A ASN* 1.3 75.4 - - - +
260A MET* 1.3 62.6 + - - +
262A LEU* 3.2 7.7 + - - +
263A LEU* 3.0 30.2 + - + +
296B LEU* 4.4 7.2 - - + -
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Residues in contact with MET 260 (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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156A TRP* 3.4 43.3 - - + +
187A PRO* 4.4 15.9 - - + -
235A ILE* 4.4 12.1 - - + -
238A ALA* 4.2 14.6 - - + -
256A GLU* 2.8 20.4 + - + +
257A ALA* 3.7 5.8 - - - +
259A VAL* 1.3 72.4 - - - +
261A GLN* 1.3 59.0 + - - +
264A LEU* 2.9 49.9 + - + +
273A VAL* 3.6 27.6 - - + -
275A PHE* 3.7 26.2 - - + -
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Residues in contact with GLN 261 (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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257A ALA* 2.8 28.6 + - - +
258A ASN* 3.8 5.1 - - - +
259A VAL 3.3 0.2 - - - -
260A MET* 1.3 71.3 - - - +
262A LEU* 1.3 60.8 + - - +
265A GLU* 2.7 64.9 + - - +
266A GLY 3.2 0.7 + - - -
273A VAL* 3.3 29.8 + - + +
275A PHE* 4.8 0.8 - - - +
295A SER* 3.1 31.5 + - - +
297A TYR* 4.1 3.9 - - + -
307A HIS* 3.7 8.7 - - + -
308A ARG 3.9 3.4 + - - -
309A ALA* 3.0 35.2 + - - +
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Residues in contact with LEU 262 (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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171A PHE* 4.1 13.5 - - + -
182A LEU* 4.1 11.4 - - + -
258A ASN 3.0 17.2 + - - +
259A VAL* 3.2 5.4 + - - +
261A GLN* 1.3 77.1 - - - +
263A LEU* 1.3 76.8 + - + +
266A GLY* 3.0 26.0 + - - -
267A LYS* 3.1 11.9 + - + +
297A TYR* 4.0 29.6 - - + +
296B LEU* 3.9 36.6 - - + +
299B LEU* 4.1 22.4 - - + -
300B ALA* 4.7 5.2 - - + +
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Residues in contact with LEU 263 (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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156A TRP* 3.9 19.3 - - + -
168A ILE* 4.1 35.9 - - + -
171A PHE* 3.9 29.8 - - + -
172A ARG* 4.7 4.0 - - + +
182A LEU* 4.5 7.2 - - + +
184A THR* 3.6 31.4 - - + -
259A VAL* 3.0 22.4 + - + +
262A LEU* 1.3 87.9 - - + +
264A LEU* 1.3 58.8 + - - +
267A LYS* 3.1 13.2 + - + +
268A LEU* 3.0 30.1 + - - +
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Residues in contact with LEU 264 (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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156A TRP* 3.8 28.0 - - + -
160A LEU* 4.2 6.5 - - + -
232A PRO* 3.9 34.8 - - + +
235A ILE* 4.3 13.7 - - + -
260A MET* 2.9 43.2 + - + +
263A LEU* 1.3 74.3 - - - +
265A GLU* 1.3 59.8 + - - +
268A LEU* 3.5 14.6 - - + +
269A GLY 3.2 6.8 + - - -
270A ALA* 2.8 32.0 + - + +
273A VAL* 3.8 22.2 - - + -
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLN* 2.7 34.6 + - - +
264A LEU* 1.3 71.3 - - - +
266A GLY* 1.3 61.3 + - - +
269A GLY* 3.2 20.6 + - - -
270A ALA 3.6 11.7 - - - +
271A PRO 3.7 14.8 - - - +
272A LYS* 3.7 9.4 + - - -
273A VAL* 2.9 28.1 + - + -
297A TYR* 3.7 23.6 + - + +
304A SER* 5.9 1.2 - - - -
305A ALA 5.5 0.9 - - - +
307A HIS* 2.8 38.8 + - - -
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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