Contacts of the helix formed by residues 211 - 233 (chain A) in PDB entry 2M1W
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 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 5.4 1.3 - - - -
134A TRP* 4.7 0.3 - - - -
207A GLU 2.7 18.9 + - - +
208A ARG* 3.2 28.0 + - - +
209A ILE 3.4 2.2 + - - -
210A PHE* 1.3 75.0 - - - +
212A GLU* 1.3 53.1 + - - +
213A SER* 2.7 28.1 + - - +
214A VAL* 2.6 32.5 + - + +
215A TYR* 2.6 33.2 + - - +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS* 5.5 1.9 - - - +
210A PHE 4.3 0.6 + - - -
211A GLN* 1.3 67.1 - - - +
213A SER* 1.3 57.3 + - - +
214A VAL 2.7 6.8 + - - -
215A TYR* 2.5 36.1 + - + +
216A LYS* 2.9 49.4 + - + +
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Residues in contact with SER 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLN* 2.7 27.8 + - - +
212A GLU* 1.3 78.2 - - - +
214A VAL* 1.3 58.6 + - - +
216A LYS* 4.1 8.9 + - - +
217A THR* 3.8 17.2 + - - -
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TRP* 3.4 32.3 - - + +
208A ARG 3.9 5.2 - - - +
209A ILE 3.5 6.7 - - - +
211A GLN* 2.6 42.9 + - + +
213A SER* 1.3 73.3 - - - +
215A TYR* 1.3 62.7 + - - -
216A LYS 3.0 2.2 - - - -
217A THR* 3.4 5.8 + - - +
218A GLN* 3.0 38.0 + - + +
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Residues in contact with TYR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 3.8 33.3 - - - -
79A LEU 5.6 0.2 - - - -
80A LYS* 4.1 44.1 - - + +
107A LYS 5.4 1.0 + - - -
108A PRO* 5.7 0.2 - - - +
133A ALA* 5.8 2.0 - - + -
134A TRP* 4.9 6.5 - + + -
211A GLN 2.6 12.6 + - - +
212A GLU* 2.5 25.9 + - + +
214A VAL* 1.3 73.2 - - - +
216A LYS* 1.3 73.7 + - - -
218A GLN* 3.9 7.2 + - + -
219A GLN* 3.0 37.5 + - + +
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Residues in contact with LYS 216 (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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212A GLU* 2.9 53.6 + - + +
213A SER* 4.2 9.2 - - - +
215A TYR* 1.3 92.5 - - + +
217A THR* 1.3 56.0 + - - +
219A GLN* 2.5 29.9 + - + +
220A THR* 2.6 23.4 + - - +
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Residues in contact with THR 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A HIS 5.4 0.2 - - - +
213A SER 3.8 10.8 + - - -
214A VAL* 3.4 9.7 + - - -
216A LYS* 1.3 76.1 - - - +
218A GLN* 1.3 55.4 - - - +
220A THR* 3.0 7.3 + - - +
221A ILE* 2.7 65.0 + - + +
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Residues in contact with GLN 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER 4.5 2.5 - - - +
133A ALA* 2.8 36.6 - - + +
134A TRP* 4.2 1.8 + - - -
165A HIS 3.3 10.3 + - - -
166A LYS 2.8 22.4 + - - +
167A TYR* 2.4 29.5 + - - +
169A SER* 4.0 4.9 - - - -
214A VAL* 3.0 32.6 + - + +
215A TYR* 4.1 6.1 - - + +
217A THR* 1.3 78.3 - - - +
219A GLN* 1.3 56.7 + - - +
221A ILE* 3.5 10.7 - - - +
222A TRP* 3.2 27.9 + - - +
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Residues in contact with GLN 219 (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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78A PHE* 4.3 13.0 - - - +
215A TYR* 3.0 36.0 + - + +
216A LYS* 2.5 17.9 + - + +
218A GLN* 1.3 74.4 - - - +
220A THR* 1.3 59.2 + - - +
221A ILE 3.4 0.2 - - - -
222A TRP* 3.9 19.4 - - - -
223A LYS* 2.9 35.3 + - - +
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Residues in contact with THR 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LYS* 2.6 20.1 + - - +
217A THR* 3.7 8.5 - - - -
219A GLN* 1.3 76.5 - - - +
221A ILE* 1.3 61.4 + - + +
222A TRP 3.3 0.4 - - - -
223A LYS* 3.2 14.0 - - + +
224A GLU* 3.0 40.6 + - + +
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A HIS 3.5 11.0 - - - +
166A LYS* 3.6 12.3 - - + -
167A TYR* 2.9 36.3 - - + +
217A THR* 2.7 52.6 + - + +
218A GLN* 3.5 17.5 - - - +
220A THR* 1.3 75.5 - - + +
222A TRP* 1.3 56.3 + - - +
224A GLU* 3.6 5.3 - - - +
225A THR* 2.8 31.2 + - - -
228A MET* 4.2 6.5 - - + +
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Residues in contact with TRP 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 3.4 35.7 + - + -
77A VAL* 2.9 33.2 - - - -
78A PHE* 3.3 24.2 - - + -
131A GLY* 3.0 36.1 - - - +
132A SER 5.5 0.4 - - - +
167A TYR* 3.6 12.8 - + + +
218A GLN 3.2 20.7 + - - +
219A GLN* 3.9 21.1 - - - +
221A ILE* 1.3 74.8 - - - +
223A LYS* 1.3 61.1 + - - +
224A GLU 2.7 5.8 + - - -
225A THR* 2.6 45.9 + - + +
226A ARG* 2.9 29.5 - - - +
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Residues in contact with LYS 223 (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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219A GLN* 2.9 38.0 + - + +
220A THR* 3.2 25.1 - - + +
222A TRP* 1.3 80.2 - - + +
224A GLU* 1.3 78.7 + - + +
226A ARG* 3.4 43.0 + - - +
227A ASN* 3.9 9.7 + - - -
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A THR* 3.0 28.8 + - + +
221A ILE* 3.6 7.0 - - - +
222A TRP 2.8 0.6 - - - -
223A LYS* 1.3 97.6 + - + +
225A THR* 1.3 57.0 + - - +
226A ARG 2.9 5.2 - - - -
227A ASN* 2.8 41.2 + - - +
228A MET* 2.8 28.4 - - + +
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Residues in contact with THR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TYR* 3.4 27.7 + - + -
221A ILE 2.8 15.3 + - - -
222A TRP* 2.6 46.5 + - + +
224A GLU* 1.3 73.0 - - - +
226A ARG* 1.3 50.8 + - + +
227A ASN 3.1 1.2 + - - -
228A MET* 3.3 17.1 - - - +
229A VAL* 2.6 52.1 + - + +
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Residues in contact with ARG 226 (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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76A GLU* 4.1 20.4 + - - +
222A TRP* 2.9 41.1 - - - +
223A LYS* 3.4 33.2 + - - +
224A GLU 2.9 0.4 - - - -
225A THR* 1.3 80.9 - - + +
227A ASN* 1.3 64.8 + - - +
229A VAL* 3.3 11.4 - - - +
230A GLN* 3.0 28.0 - - - +
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Residues in contact with ASN 227 (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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223A LYS 3.9 12.3 + - - -
224A GLU* 2.8 31.2 + - - +
226A ARG* 1.3 85.6 + - - +
228A MET* 1.3 57.5 + - - +
229A VAL 2.9 0.9 - - - -
230A GLN* 2.7 6.3 + - - +
231A ARG* 2.5 39.9 + - + +
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Residues in contact with MET 228 (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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166A LYS* 6.4 1.8 - - + -
221A ILE* 4.2 7.2 - - + +
224A GLU* 2.8 35.0 - - + +
225A THR* 3.3 34.8 - - - +
227A ASN* 1.3 76.3 - - - +
229A VAL* 1.3 62.3 + - + +
231A ARG* 3.8 8.1 - - - -
232A GLN 3.1 10.0 + - - -
233A PHE* 2.9 35.5 + - + +
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A THR* 2.6 39.9 - - + +
226A ARG* 3.3 17.9 - - - +
227A ASN 2.8 1.4 + - - -
228A MET* 1.3 76.9 - - + +
230A GLN* 1.3 72.5 + - + +
231A ARG 2.9 8.7 + - - -
232A GLN 3.9 0.2 + - - -
233A PHE* 3.2 28.6 + - + +
234A ILE* 2.6 36.9 + - + +
235A ALA 5.0 2.0 - - - +
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Residues in contact with GLN 230 (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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72A LEU* 4.6 13.5 + - - +
226A ARG* 3.0 21.1 - - - +
227A ASN* 2.7 7.5 + - - +
229A VAL* 1.3 79.8 - - - +
231A ARG* 1.3 61.5 + - - +
234A ILE* 3.9 26.1 - - - +
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Residues in contact with ARG 231 (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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227A ASN 2.5 20.2 + - - +
228A MET* 3.4 11.0 - - - +
229A VAL 2.9 2.1 - - - -
230A GLN* 1.3 78.8 - - - +
232A GLN* 1.3 85.2 + - + +
233A PHE 3.7 0.4 - - - -
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Residues in contact with GLN 232 (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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228A MET 3.1 1.0 + - - -
231A ARG* 1.3 102.4 + - + +
233A PHE* 1.3 71.4 + - - +
234A ILE 3.8 1.3 - - - +
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Residues in contact with PHE 233 (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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228A MET* 2.9 27.6 + - + +
229A VAL* 3.2 21.2 - - + +
232A GLN* 1.3 84.4 - - - +
234A ILE* 1.3 69.3 + - - +
235A ALA* 3.6 1.0 + - - -
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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