Contacts of the helix formed by residues 285 - 300 (chain B) in PDB entry 2XMR
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 GLN 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274B MET* 3.5 23.8 - - + +
275B ALA 2.8 28.1 + - - +
276B ASP* 3.6 12.9 + - - +
277B SER* 3.3 17.6 - - - -
281B PRO 3.0 9.9 + - - +
284B THR* 1.3 95.3 - - - +
286B PRO* 1.4 67.8 - - - +
287B GLY 3.1 3.5 + - - +
288B LYS* 3.4 16.2 + - + +
289B LEU* 3.1 21.0 + - - +
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Residues in contact with PRO 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO* 5.2 4.5 - - + +
68B LEU* 3.7 28.6 - - + +
71B PHE* 4.1 31.0 - - + -
281B PRO 4.1 0.6 - - - +
282B GLN 4.3 8.3 - - - +
283B LEU 4.0 13.2 - - - +
284B THR 3.5 6.3 - - - +
285B GLN* 1.4 89.8 - - - +
287B GLY* 1.3 53.1 + - - +
289B LEU* 3.9 1.3 - - + +
290B THR* 2.7 42.0 + - - -
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Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.5 23.5 - - - -
73B ASP* 4.8 5.9 - - - +
285B GLN* 3.1 1.4 - - - +
286B PRO* 1.3 84.3 - - - +
288B LYS* 1.3 60.7 + - - +
290B THR* 3.7 2.6 - - - -
291B GLU* 3.2 23.1 + - - +
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Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 5.6 2.0 - - + -
274B MET* 3.6 33.7 - - + -
275B ALA* 5.1 10.7 + - - +
285B GLN* 3.4 19.2 + - + +
287B GLY* 1.3 71.6 - - - +
289B LEU* 1.3 59.9 + - - +
291B GLU* 3.3 9.0 + - - +
292B ALA* 3.0 26.2 + - - +
175C LEU* 3.2 48.0 + - + +
176C THR* 5.0 3.7 - - + +
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.0 18.4 - - + -
74B MET* 5.6 1.1 - - + -
153B VAL* 5.1 3.6 - - + -
155B ILE* 4.2 14.8 - - + -
244B MET* 4.5 8.7 - - + -
246B VAL* 4.3 19.7 - - + -
272B LEU* 4.2 20.2 - - + -
274B MET* 4.2 9.5 - - - +
281B PRO* 4.5 4.3 - - + +
282B GLN* 3.6 39.3 - - + +
285B GLN 3.1 17.3 + - - +
286B PRO* 3.9 3.6 - - + +
288B LYS* 1.3 74.5 - - - +
290B THR* 1.3 59.7 + - - +
292B ALA* 3.3 4.3 + - - +
293B PHE* 2.8 29.9 + - + +
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 3.8 2.4 - - - +
71B PHE* 3.8 10.0 - - - -
73B ASP* 3.6 21.1 - - + +
74B MET* 3.5 51.2 - - + +
77B ILE* 3.7 14.2 - - + +
286B PRO 2.7 29.1 + - - -
287B GLY 3.7 4.9 - - - -
289B LEU* 1.3 72.4 - - - +
291B GLU* 1.3 59.4 + - - +
293B PHE* 3.1 3.2 + - - +
294B LYS* 2.8 25.5 + - + +
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Residues in contact with GLU 291 (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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287B GLY 3.2 12.5 + - - +
288B LYS* 3.7 9.8 - - - +
289B LEU 3.3 0.2 - - - -
290B THR* 1.3 79.3 - - - +
292B ALA* 1.3 63.7 + - - +
294B LYS* 3.2 17.2 + - - +
295B TYR* 2.8 60.2 + - + +
175C LEU* 3.9 22.2 - - + +
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Residues in contact with ALA 292 (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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244B MET* 4.0 7.2 - - + -
272B LEU* 3.6 29.8 - - + -
288B LYS 3.0 14.1 + - - +
289B LEU 3.4 8.7 - - - +
291B GLU* 1.3 76.1 - - - +
293B PHE* 1.3 56.5 + - - +
295B TYR* 3.2 2.1 + - - -
296B PHE* 2.9 26.0 + - - +
172C LEU* 3.4 21.2 - - + +
175C LEU* 3.5 17.3 - - + +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 4.2 17.0 - - + -
69B PHE* 5.3 2.7 - + - -
74B MET* 3.7 17.9 - - + -
77B ILE* 3.7 19.3 - - + -
78B ILE* 4.2 17.7 - - + -
127B ILE* 4.4 7.2 - - + -
129B VAL* 4.3 17.9 - - + -
153B VAL* 3.6 32.8 - - + -
244B MET* 4.0 5.8 - - + +
289B LEU* 2.8 19.1 + - + +
290B THR* 3.4 10.5 - - - +
292B ALA* 1.3 70.1 - - - +
294B LYS* 1.3 65.4 + - - +
296B PHE* 3.4 16.2 + + + +
297B LEU* 3.0 54.3 + - + +
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.6 28.3 - - - +
77B ILE* 3.7 34.4 - - + +
290B THR 2.8 12.2 + - - +
291B GLU* 3.2 16.3 + - - +
293B PHE* 1.3 77.6 - - - +
295B TYR* 1.3 81.6 + - - +
297B LEU* 3.4 4.8 + - - +
298B GLN* 3.0 48.7 + - + +
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Residues in contact with TYR 295 (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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119A GLN* 3.9 9.4 - - - +
291B GLU* 2.8 55.0 + - + +
292B ALA* 3.2 0.9 + - - +
294B LYS* 1.3 93.3 + - - +
296B PHE* 1.3 60.3 + - - +
298B GLN* 3.7 15.9 - - - -
299B GLY* 2.9 24.3 + - - -
168C ALA* 3.5 20.6 - - - +
171C LYS* 3.7 59.6 + - + +
172C LEU* 3.6 20.6 - - + +
175C LEU* 4.2 9.6 - - + -
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Residues in contact with PHE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 4.4 7.6 - - + -
151B GLY* 4.2 1.1 - - - -
152B LEU 3.4 16.6 - - - -
153B VAL* 3.9 24.2 - - + -
242B PRO* 3.4 39.5 - - + -
243B VAL 3.8 6.7 - - - -
244B MET* 3.7 35.4 - - + -
268B GLN 5.5 0.2 - - - -
270B SER* 4.3 6.5 - - - -
292B ALA 2.9 16.9 + - - +
293B PHE* 3.5 17.3 - + - +
294B LYS 3.2 0.2 - - - -
295B TYR* 1.3 76.4 - - - +
297B LEU* 1.3 63.7 + - + +
299B GLY* 3.3 4.7 + - - -
300B MET* 3.2 37.5 + - - +
172C LEU* 4.1 7.5 - - + +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 5.3 0.7 - - + -
77B ILE* 4.6 15.3 - - + +
78B ILE* 5.5 0.2 - - + -
81B PHE* 3.9 28.9 - - + -
127B ILE* 3.7 30.5 - - + -
293B PHE* 3.0 54.1 + - + +
294B LYS* 3.7 4.3 - - - +
296B PHE* 1.3 75.4 - - + +
298B GLN* 1.3 64.6 + - + +
300B MET* 3.0 20.2 + - - +
301B GLY 3.2 0.2 + - - -
302B TYR* 2.9 37.1 + - + +
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Residues in contact with GLN 298 (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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115A PRO* 4.4 4.0 - - - +
119A GLN* 2.7 44.2 + - - +
145A HIS* 6.0 2.6 - - - -
294B LYS* 3.0 35.4 + - + +
295B TYR* 3.7 18.7 - - - +
297B LEU* 1.3 75.5 - - + +
299B GLY* 1.3 58.9 + - - +
301B GLY* 2.9 17.3 + - - -
302B TYR 3.5 19.7 - - - +
303B MET* 4.3 28.4 + - - +
164C TRP* 3.3 14.8 - - - -
168C ALA* 4.5 7.3 - - + +
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Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PRO* 6.1 0.4 - - - +
295B TYR 2.9 12.8 + - - -
296B PHE* 3.3 6.3 + - - -
297B LEU 3.2 0.2 - - - -
298B GLN* 1.3 75.7 - - - +
300B MET* 1.3 58.0 - - - +
301B GLY 3.2 0.8 + - - -
164C TRP* 3.6 8.3 - - - -
165C MET* 3.3 32.3 - - - +
168C ALA* 3.7 19.6 - - - +
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Residues in contact with MET 300 (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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127B ILE* 3.7 20.9 - - + -
150B GLU* 3.9 25.8 - - + +
151B GLY* 4.3 2.9 - - - -
242B PRO* 3.9 23.8 - - + -
296B PHE* 3.2 39.4 + - + +
297B LEU* 3.0 14.8 + - - +
299B GLY* 1.3 77.6 - - - +
301B GLY* 1.3 57.0 + - - +
302B TYR* 3.1 36.5 + - + -
164C TRP* 4.4 3.6 - - - -
165C MET* 5.4 1.3 - - - -
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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