Contacts of the helix formed by residues 212 - 226 (chain C) 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 ASN 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C GLY 2.9 20.3 + - - +
91C MET* 3.7 9.9 - - - +
92C GLU 5.1 2.3 + - - -
95C ALA* 4.7 10.7 - - + +
97C VAL* 4.5 6.3 - - + -
210C ALA* 3.7 4.0 - - - +
211C PRO* 1.3 80.1 - - + +
213C LEU* 1.3 62.5 + - - -
214C ASP 3.2 3.4 - - - +
215C ASN* 3.0 30.8 + - - +
216C ILE* 3.1 12.3 + - - +
1306C GOL 2.7 45.6 + - - -
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ILE* 4.8 10.5 - - + -
180C PRO* 3.9 29.2 - - + -
183C ILE* 4.9 0.4 - - + -
207C ILE* 3.7 18.4 - - + +
208C THR 3.9 20.2 - - - +
210C ALA* 3.3 19.9 + - + +
211C PRO 3.4 2.0 + - - -
212C ASN* 1.3 77.1 + - - +
214C ASP* 1.3 62.0 + - - +
216C ILE* 3.2 23.8 + - + -
217C GLU* 2.9 27.6 + - + +
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Residues in contact with ASP 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C VAL* 4.0 23.5 - - + +
100C LEU* 5.9 2.9 - - - +
211C PRO 5.3 0.6 + - - -
212C ASN 3.2 0.8 - - - -
213C LEU* 1.3 82.9 - - - +
215C ASN* 1.3 61.2 + - - +
217C GLU* 3.6 18.6 - - - +
218C LEU* 3.3 26.1 + - - +
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Residues in contact with ASN 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLY* 2.9 32.6 + - - +
91C MET* 3.3 14.3 - - + +
95C ALA* 4.7 0.2 - - - +
96C PRO 3.0 23.4 + - - -
97C VAL* 3.5 10.3 - - - +
98C PHE* 3.1 37.3 + - + +
104C TYR* 4.7 0.5 - - - -
212C ASN* 3.0 19.8 + - - +
214C ASP* 1.3 75.4 - - - +
216C ILE* 1.3 65.0 + - - +
218C LEU* 3.0 22.8 + - - +
219C TYR 3.2 8.8 + - - -
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Residues in contact with ILE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C VAL* 4.1 0.6 - - + +
58C GLY* 3.7 31.6 - - - +
91C MET* 3.8 23.1 - - - +
183C ILE* 3.5 27.6 - - + -
207C ILE* 5.0 5.2 - - + +
210C ALA* 3.8 19.5 - - + -
212C ASN* 3.1 14.2 + - - +
213C LEU* 3.4 18.2 - - + +
215C ASN* 1.3 77.8 - - - +
217C GLU* 1.3 57.6 + - - +
219C TYR* 3.2 5.3 + - - +
220C TRP* 2.9 26.9 + - - +
1306C GOL 3.7 29.2 - - - +
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Residues in contact with GLU 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ILE* 3.3 45.0 - - + +
213C LEU* 2.9 16.5 + - + +
214C ASP* 3.6 19.7 - - - +
215C ASN 3.1 0.4 - - - -
216C ILE* 1.3 78.8 - - - +
218C LEU* 1.3 60.0 + - + +
220C TRP* 3.3 10.0 - - + +
221C ASN* 2.9 43.2 + - - +
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C PHE* 4.2 22.9 - - + -
99C PRO 5.7 0.7 - - - +
102C TYR* 4.3 23.1 - - + +
104C TYR* 3.6 38.0 - - + +
214C ASP 3.3 18.4 - - - +
215C ASN* 3.0 8.3 + - - +
217C GLU* 1.3 79.5 - - + +
219C TYR* 1.3 59.2 + - - +
221C ASN* 3.4 16.5 + - - +
222C SER* 3.0 29.3 + - - -
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Residues in contact with TYR 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TYR* 3.6 3.5 - - - -
55C HIS* 2.9 35.3 + + - -
56C ASP 3.7 7.2 - - - -
57C VAL* 3.7 31.9 - - + -
58C GLY 4.6 2.5 - - - -
88C ALA* 4.2 8.5 - - + -
91C MET* 3.7 24.0 - - + -
104C TYR* 3.7 15.0 - + + -
107C LEU* 3.9 8.5 - - + -
110C LEU* 3.8 29.2 - - + -
133C ALA* 3.5 25.9 - - + +
134C GLY 3.6 0.2 + - - -
137C ILE* 3.6 12.7 - - + +
215C ASN 3.2 2.4 + - - -
216C ILE* 3.5 8.1 - - - +
218C LEU* 1.3 75.8 - - - +
220C TRP* 1.3 55.3 + - - +
222C SER* 3.2 2.7 + - - -
223C TYR* 2.8 32.4 + - - +
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Residues in contact with TRP 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C VAL* 3.6 26.3 - - + +
170C HIS* 3.9 19.7 + + - -
179C ILE* 4.2 25.2 - - + +
182C MET* 3.8 41.6 - - + +
183C ILE* 3.8 17.2 - - + +
186C HIS* 3.6 30.7 - + + -
216C ILE 2.9 14.0 + - - +
217C GLU* 3.3 14.8 - - + +
219C TYR* 1.3 73.9 - - - +
221C ASN* 1.3 65.5 + - - +
223C TYR* 3.3 14.7 + + - +
224C ASN* 3.0 65.7 + - - +
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Residues in contact with ASN 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C GLU* 2.9 36.4 + - - +
218C LEU* 3.6 20.3 - - - +
219C TYR 3.3 0.2 - - - -
220C TRP* 1.3 81.8 - - - +
222C SER* 1.3 62.7 + - - +
224C ASN* 3.3 6.7 + - - +
225C ASN* 2.9 41.6 + - - +
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Residues in contact with SER 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C TYR* 3.7 7.2 + - - +
105C PRO 2.5 31.3 + - - -
106C SER* 3.8 4.1 - - - +
107C LEU* 3.7 28.0 + - - +
218C LEU 3.0 15.0 + - - -
219C TYR* 3.4 12.1 - - - -
221C ASN* 1.3 74.5 - - - +
223C TYR* 1.3 64.9 + - - +
225C ASN* 3.3 15.4 + - - +
226C ARG* 3.3 9.7 + - - -
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Residues in contact with TYR 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C VAL* 3.8 14.6 - - + -
107C LEU* 3.9 10.8 - - + +
132C GLY 4.7 3.1 - - - -
133C ALA* 3.6 36.1 - - + -
136C TYR* 5.3 2.5 - - + -
156C ASN 5.3 1.2 + - - -
158C ASP* 3.8 11.2 + - + +
162C LYS* 5.4 1.3 - - - -
186C HIS* 3.6 28.8 - + - -
219C TYR 2.8 16.5 + - - +
220C TRP* 3.4 19.1 - + - +
222C SER* 1.3 73.0 - - - +
224C ASN* 1.3 79.4 + - - +
225C ASN 3.2 0.9 + - - -
226C ARG* 2.9 74.9 + - - +
253C HIS* 3.8 13.9 - + - -
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Residues in contact with ASN 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C LYS* 3.2 35.6 + - - +
167C TRP* 3.4 24.7 - - + -
170C HIS* 3.4 17.6 + - + +
220C TRP* 3.0 60.8 + - - +
221C ASN* 3.8 8.0 - - - +
223C TYR* 1.3 90.0 - - - +
225C ASN* 1.3 64.6 + - - +
226C ARG* 3.7 6.9 + - - +
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Residues in contact with ASN 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A HIS* 5.6 1.2 - - - -
28A SER 4.6 5.7 - - - +
120A TYR* 3.3 45.8 + - + +
167C TRP* 3.4 21.4 - - - -
221C ASN* 2.9 34.0 + - - +
222C SER* 3.3 8.0 + - - +
223C TYR 3.1 0.6 - - - -
224C ASN* 1.3 77.3 - - - +
226C ARG* 1.3 66.8 + - - +
227C ARG* 3.7 6.6 + - - +
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Residues in contact with ARG 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A SER 5.5 0.9 - - - +
107C LEU* 3.8 21.5 - - + +
136C TYR* 3.6 30.7 - - + -
158C ASP* 3.1 43.4 + - - -
160C ASN 3.0 23.5 + - - +
161C ALA* 3.3 17.9 - - - +
162C LYS* 4.6 17.1 + - - +
222C SER 3.3 5.2 + - - +
223C TYR* 2.9 60.3 + - - +
224C ASN* 4.1 10.6 + - - +
225C ASN* 1.3 80.5 - - - +
227C ARG* 1.3 60.6 + - - +
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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