Contacts of the helix formed by residues 205 - 217 (chain M) in PDB entry 2ZHX
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 ARG 205 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47K SER 3.4 20.0 + - - -
48K ASN* 2.5 36.4 + - - +
51K ARG* 3.5 43.9 - - - +
54K THR* 4.2 18.8 + - - +
100M GLU* 3.1 26.0 + - - -
103M ALA* 3.9 26.0 + - - +
104M ASP* 3.1 38.2 - - - +
203M GLY* 3.5 15.6 - - - +
204M SER* 1.3 75.0 - - - +
206M PRO* 1.3 70.0 - - - +
208M SER* 4.2 3.8 - - - +
209M ARG* 3.0 27.1 + - + +
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Residues in contact with PRO 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100M GLU* 3.7 17.7 - - + +
104M ASP* 4.0 2.5 - - - +
166M ILE* 4.3 16.6 - - + -
168M TRP* 4.6 15.0 - - + +
187M ILE* 3.9 21.8 - - + +
201M PHE* 4.7 3.8 - - + -
204M SER* 3.2 21.1 - - - +
205M ARG* 1.3 88.5 - - - +
207M PHE* 1.3 76.3 + - + +
209M ARG* 3.1 0.9 + - + +
210M ALA* 2.6 40.1 + - - +
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Residues in contact with PHE 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M ILE* 5.1 0.7 - - + -
97M ILE* 3.6 28.5 - - + -
100M GLU* 4.1 2.9 - - + -
101M TYR* 3.3 44.9 - + + -
104M ASP* 3.2 13.2 + - + +
105M LEU* 4.2 9.6 - - + -
118M TRP* 3.6 26.2 - + - -
166M ILE* 5.0 3.6 - - + -
168M TRP* 4.8 9.2 - + - -
201M PHE* 5.8 0.4 - + - -
206M PRO* 1.3 91.2 - - + +
208M SER* 1.3 64.0 + - - +
210M ALA* 3.3 2.4 + - - +
211M ASN* 3.0 16.8 + - - +
224M TRP* 3.3 59.4 + + + +
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Residues in contact with SER 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M ASP* 2.7 34.0 + - - -
105M LEU* 4.1 13.2 - - - +
205M ARG* 3.7 5.2 + - - +
207M PHE* 1.3 74.3 - - - +
209M ARG* 1.3 54.8 + - - +
211M ASN* 2.9 12.1 + - - +
212M GLU* 2.6 53.1 + - - +
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Residues in contact with ARG 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K ARG* 4.7 4.3 - - - +
77K VAL* 5.8 4.3 - - + -
85K PRO* 4.4 7.2 - - + +
114K ASP* 2.6 42.8 + - - -
116K THR* 3.6 28.0 + - - +
117K PRO* 4.5 5.7 - - - +
120K GLN* 4.0 7.1 + - - -
187M ILE* 4.3 35.5 - - + +
188M GLU 4.6 5.5 + - - -
204M SER* 2.6 39.6 + - - +
205M ARG* 3.0 23.6 + - + +
206M PRO* 3.6 3.6 - - + +
208M SER* 1.3 77.4 + - - +
210M ALA* 1.3 63.3 + - - +
212M GLU* 3.4 17.1 + - - +
213M LEU* 2.9 32.9 + - + +
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Residues in contact with ALA 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62M VAL* 4.5 7.9 - - + -
164M VAL* 3.7 30.4 - - + +
166M ILE* 4.6 10.1 - - + -
187M ILE* 4.4 1.3 - - + +
206M PRO 2.6 21.6 + - - +
207M PHE 3.4 5.4 - - - +
209M ARG* 1.3 71.6 - - - +
211M ASN* 1.3 63.5 + - - +
213M LEU* 3.0 6.6 + - - +
214M LEU* 2.8 26.4 + - - +
224M TRP* 4.4 14.8 - - + -
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Residues in contact with ASN 211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105M LEU* 5.1 3.2 - - - +
207M PHE 3.0 7.6 + - - +
208M SER* 2.9 13.3 + - - +
210M ALA* 1.3 76.7 - - - +
212M GLU* 1.3 63.9 + - + +
214M LEU* 3.1 10.7 + - - +
215M VAL* 3.0 27.0 + - - +
221M PRO* 3.4 16.5 - - + +
222M ILE* 2.7 40.2 + - - +
223M ASP 5.1 0.2 + - - -
224M TRP* 3.0 32.7 + - - +
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Residues in contact with GLU 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74K GLY 5.5 0.2 - - - +
77K VAL* 5.0 5.9 - - - +
84K ALA* 3.5 18.6 - - - +
85K PRO* 3.3 24.3 - - + +
86K ASP* 3.3 31.5 - - - +
208M SER* 2.6 40.8 + - - +
209M ARG* 3.7 14.7 - - - +
211M ASN* 1.3 74.2 - - + +
213M LEU* 1.3 62.4 + - - +
215M VAL* 3.3 5.5 + - - +
216M GLY 3.1 17.3 + - - -
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Residues in contact with LEU 213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85K PRO* 3.3 29.1 - - + +
112K ASN* 3.5 17.9 - - - +
114K ASP* 6.2 0.2 - - - +
164M VAL* 3.8 22.4 - - + -
185M VAL* 4.2 22.4 - - + -
187M ILE* 3.5 31.9 - - + -
209M ARG* 2.9 25.8 + - + +
210M ALA 3.2 6.1 - - - +
212M GLU* 1.3 76.1 - - - +
214M LEU* 1.3 64.6 + - - +
216M GLY* 3.0 5.2 + - - -
217M MET* 3.0 30.0 + - + +
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Residues in contact with LEU 214 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M ARG* 3.8 34.1 - - + +
62M VAL* 3.8 22.9 - - + -
162M PRO* 4.5 12.1 - - + +
164M VAL* 3.8 13.2 - - + -
210M ALA 2.8 15.4 + - - +
211M ASN* 3.1 15.5 + - - +
213M LEU* 1.3 72.3 - - - +
215M VAL* 1.3 60.3 + - - +
217M MET* 3.0 14.8 + - - +
218M GLY 3.1 0.2 + - - -
219M ALA* 2.9 38.1 + - + +
220M GLU 3.4 24.7 - - - +
222M ILE* 4.1 14.8 - - + +
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Residues in contact with VAL 215 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K ASP* 4.8 10.1 - - + +
211M ASN* 3.0 17.2 + - + +
212M GLU* 3.8 7.0 - - - +
214M LEU* 1.3 70.4 - - - +
216M GLY* 1.3 56.5 + - - +
217M MET 3.0 4.7 - - - -
218M GLY* 2.6 22.7 + - - -
219M ALA 3.6 15.0 - - - +
221M PRO* 4.4 20.4 - - + -
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Residues in contact with GLY 216 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85K PRO 5.1 2.5 - - - -
86K ASP* 4.2 20.8 - - - +
212M GLU 3.1 10.1 + - - -
213M LEU* 3.0 9.4 + - - -
215M VAL* 1.3 76.4 - - - +
217M MET* 1.3 60.1 + - - +
218M GLY 3.8 0.2 + - - -
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Residues in contact with MET 217 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162M PRO* 3.5 37.1 - - + +
163M LEU 4.5 1.8 - - - +
164M VAL* 3.7 19.7 - - + -
183M ASN* 3.6 20.0 - - - +
185M VAL* 3.6 28.0 - - + -
213M LEU* 3.0 36.1 + - + +
214M LEU* 3.4 11.4 - - - +
215M VAL 3.0 0.6 - - - -
216M GLY* 1.3 80.3 - - - +
218M GLY* 1.3 58.0 + - - +
219M ALA 3.4 0.6 + - - -
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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