Contacts of the helix formed by residues 226 - 243 (chain H) in PDB entry 1GZ0
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 226 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C HIS* 5.4 10.7 - - - -
111C ALA* 5.8 5.9 - - + +
114C ARG* 3.6 26.9 - - - +
141C VAL* 5.4 8.0 - - + +
108H ASN* 4.5 11.2 + - - +
198H GLU* 3.9 7.2 + - - -
225H LEU* 1.3 77.9 - - - +
227H VAL* 1.3 63.6 + - - +
228H SER* 2.7 42.6 + - - -
229H VAL* 3.3 17.9 + - + +
230H ALA* 2.9 26.2 + - - +
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Residues in contact with VAL 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H VAL* 4.2 20.2 - - + -
108H ASN* 3.8 38.1 - - + +
112H CYS* 4.6 6.1 - - - -
195H MSE 4.6 9.6 - - + -
196H GLY 3.7 24.0 - - - +
197H ALA* 4.7 0.4 - - - -
198H GLU* 3.9 21.7 - - + +
225H LEU 3.6 2.2 + - - -
226H ASN* 1.3 77.7 + - - +
228H SER* 1.3 61.0 + - - +
230H ALA* 3.9 5.1 - - - +
231H THR* 2.7 42.3 + - - +
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Residues in contact with SER 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C VAL* 4.0 17.7 - - - +
108H ASN* 4.8 4.0 + - - -
111H ALA* 3.4 40.4 - - - +
112H CYS* 4.1 11.2 - - - -
115H SER* 4.4 2.8 + - - -
226H ASN* 2.7 23.1 + - - -
227H VAL* 1.3 75.1 - - - +
229H VAL* 1.3 61.1 + - - +
231H THR* 3.2 1.8 + - - -
232H GLY* 2.7 27.2 + - - -
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Residues in contact with VAL 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ALA* 5.3 4.9 - - + +
115C SER* 3.9 17.7 - - - +
228C SER* 4.2 29.8 - - - +
229C VAL* 4.1 12.1 - - + +
232C GLY* 4.2 10.5 - - - -
225H LEU* 3.6 26.2 - - + -
226H ASN* 3.3 25.5 + - + +
228H SER* 1.3 78.8 + - - +
230H ALA* 1.3 57.6 + - - +
232H GLY* 3.1 2.1 + - - -
233H ILE* 2.8 43.7 + - + +
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Residues in contact with ALA 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H THR* 5.8 0.2 - - + -
195H MSE 3.7 13.9 - - + -
216H ILE* 3.7 24.2 - - + -
225H LEU* 4.4 11.8 - - + +
226H ASN 2.9 18.7 + - - +
227H VAL* 3.9 5.6 - - - +
229H VAL* 1.3 78.3 - - - +
231H THR* 1.3 62.7 + - - +
233H ILE* 3.4 4.6 + - - +
234H CYS* 3.0 30.0 + - - -
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Residues in contact with THR 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H LEU* 4.0 26.5 - - + -
100H LEU* 4.4 0.2 - - - +
112H CYS* 3.7 24.1 - - + +
115H SER* 5.0 0.9 - - - -
195H MSE 3.4 28.1 - - + +
227H VAL* 2.7 26.2 + - - +
228H SER 3.6 3.8 - - - -
230H ALA* 1.3 74.3 - - - +
232H GLY* 1.3 60.5 + - - +
234H CYS* 3.3 1.0 + - - +
235H LEU* 2.8 55.9 + - + +
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Residues in contact with GLY 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C VAL* 3.7 18.6 - - - -
233C ILE* 3.6 9.4 - - - -
115H SER* 4.2 12.5 + - - -
228H SER 2.7 18.8 + - - -
229H VAL 3.5 2.7 - - - -
231H THR* 1.3 74.4 - - - +
233H ILE* 1.3 56.8 + - - +
235H LEU* 4.4 2.2 - - - -
236H PHE* 2.9 38.7 + - - +
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Residues in contact with ILE 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C GLY 3.6 22.4 - - - +
233C ILE* 3.8 8.2 - - - +
236C PHE* 3.5 47.8 - - + -
182H LEU* 4.4 13.5 - - + -
183H TYR* 4.4 4.5 - - - +
216H ILE* 4.8 10.3 - - + -
225H LEU* 3.7 25.6 - - + -
229H VAL* 2.8 29.5 + - + +
230H ALA* 3.7 7.0 - - - +
231H THR 3.2 0.2 - - - -
232H GLY* 1.3 72.2 - - - +
234H CYS* 1.3 58.7 + - - +
236H PHE* 3.8 1.4 - - - +
237H GLU* 3.0 25.9 + - + +
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Residues in contact with CYS 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H THR* 3.6 21.3 - - - -
182H LEU* 3.8 18.4 - - + -
187H MSE 4.0 6.5 - - + +
193H LEU* 3.7 24.5 - - + -
195H MSE 4.2 4.5 - - - -
214H ILE* 4.7 7.4 - - + -
216H ILE* 3.9 25.4 - - - -
230H ALA 3.0 21.0 + - - +
231H THR 4.0 0.7 - - - +
233H ILE* 1.3 73.6 - - - +
235H LEU* 1.3 67.2 + - - +
237H GLU* 3.3 2.9 + - - +
238H ALA* 3.2 21.3 + - - +
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Residues in contact with LEU 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H PHE* 4.1 14.1 - - + -
98H LEU* 4.0 12.1 - - + -
115H SER* 4.2 6.5 - - - -
116H ALA* 4.0 27.8 - - - +
119H ALA* 3.8 19.1 - - + -
121H VAL* 4.0 16.8 - - + -
193H LEU* 3.3 24.2 - - + -
231H THR* 2.8 42.2 + - + +
232H GLY 3.7 3.4 - - - +
234H CYS* 1.3 72.2 - - - +
236H PHE* 1.3 63.4 + - + +
238H ALA* 3.1 9.0 + - - +
239H VAL* 3.0 26.8 + - - +
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Residues in contact with PHE 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C TYR* 3.5 30.5 + + - +
216C ILE* 3.9 19.7 - - + -
217C PRO* 3.3 22.7 - - + -
218C MSE 5.3 0.2 - - - -
225C LEU* 4.2 13.2 - - + -
233C ILE* 3.4 24.7 - - + -
115H SER 4.1 6.7 - - - -
118H ALA* 3.8 28.9 - - + -
119H ALA* 3.7 20.4 - - + -
232H GLY* 2.9 25.0 + - - +
233H ILE 4.2 1.8 - - - +
235H LEU* 1.3 80.3 - - + +
237H GLU* 1.3 65.0 + - - +
238H ALA 3.0 1.6 - - - -
239H VAL* 3.1 19.5 + - + +
240H ARG* 3.0 20.1 + - - +
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Residues in contact with GLU 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C TYR* 5.8 0.7 - - - -
237C GLU* 4.6 1.6 - - - +
240C ARG* 3.8 4.9 - - - -
182H LEU* 3.5 37.6 - - + +
183H TYR* 3.6 31.7 - - + +
187H MSE 4.1 6.5 - - - -
233H ILE 3.0 10.0 + - - +
234H CYS 3.3 3.3 + - - +
236H PHE* 1.3 76.7 - - - +
238H ALA* 1.3 62.4 + - - +
240H ARG* 2.5 40.3 + - - -
241H GLN* 2.7 42.1 + - - +
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Residues in contact with ALA 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H PHE* 4.1 20.6 - - + -
187H MSE 3.9 34.7 - - + +
191H LEU* 5.0 1.3 - - + -
193H LEU* 6.2 0.4 - - + -
234H CYS 3.2 11.6 + - - +
235H LEU* 3.1 11.4 + - - +
236H PHE 3.0 0.2 - - - -
237H GLU* 1.3 77.2 - - - +
239H VAL* 1.3 58.9 + - - +
241H GLN* 3.2 2.3 + - - +
242H ARG* 2.8 41.4 + - - +
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Residues in contact with VAL 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C TYR* 4.9 4.0 - - + -
217C PRO* 4.6 21.3 - - + +
96H PHE* 4.3 6.3 - - + -
119H ALA* 3.7 37.0 - - + +
235H LEU 3.0 18.4 + - - +
236H PHE* 3.1 23.8 + - + +
238H ALA* 1.3 76.7 - - - +
240H ARG* 1.3 64.2 + - - +
242H ARG* 3.2 7.0 + - - +
243H SER* 3.0 31.1 + - - +
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Residues in contact with ARG 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C TYR* 3.4 36.8 - - + -
237C GLU* 3.2 26.5 - - - -
240C ARG* 3.0 43.3 - - - +
183H TYR 6.0 0.4 + - - -
236H PHE 3.0 12.5 + - - +
237H GLU* 2.5 44.3 + - - +
238H ALA 3.2 0.2 - - - -
239H VAL* 1.3 79.0 - - - +
241H GLN* 1.3 78.3 + - - +
243H SER* 3.5 19.2 + - - +
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Residues in contact with GLN 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H LEU 3.7 9.5 + - - -
183H TYR 4.6 4.6 + - - -
185H SER 2.9 21.0 + - - +
186H LYS* 3.6 2.4 - - - -
187H MSE 2.7 39.5 + - + +
188H THR* 3.4 21.6 + - + +
237H GLU* 2.7 24.0 + - - +
238H ALA* 3.2 8.4 + - - +
240H ARG* 1.3 101.0 - - - +
242H ARG* 1.3 61.2 + - + +
243H SER* 3.4 3.3 + - - +
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Residues in contact with ARG 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H GLN* 3.7 22.4 + - - +
95H PRO 3.5 14.6 + - - -
96H PHE* 3.4 40.3 - - - +
122H HIS* 5.8 0.2 - - - -
187H MSE 3.3 26.2 + - - +
188H THR* 3.9 12.4 - - - +
189H GLY 2.6 32.8 + - - +
191H LEU* 4.6 3.2 - - - +
238H ALA* 2.8 29.3 + - - +
239H VAL* 3.2 4.7 + - - +
241H GLN* 1.3 79.5 - - - +
243H SER* 1.3 63.1 + - - +
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Residues in contact with SER 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C TYR* 5.2 5.7 - - - +
217C PRO* 6.0 1.7 - - - +
239H VAL* 3.0 23.1 + - - +
240H ARG* 3.5 14.1 + - - +
241H GLN 3.4 4.2 - - - +
242H ARG* 1.3 82.4 - - - +
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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
------------------------------------------------------------
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