Contacts of the helix formed by residues 212 - 224 (chain A) in PDB entry 4GR0
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 LEU 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A MET* 3.9 37.9 - - + -
130A VAL* 3.9 27.6 - - + +
133A ALA* 4.0 14.4 - - + -
134A ILE* 4.5 9.2 - - + -
163A PHE* 4.0 18.8 - - + -
197A PHE* 3.8 32.1 - - + -
203A TRP* 3.9 17.5 - - + -
204A THR 3.1 10.1 + - - +
210A THR 3.3 2.8 + - - -
211A ASN* 1.3 68.6 - - - +
213A PHE* 1.3 61.4 + - - +
215A THR 3.4 0.7 + - - -
216A ALA* 2.8 28.9 + - - +
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Residues in contact with PHE 213 (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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133A ALA* 3.7 36.9 - - + +
136A LYS* 3.6 20.4 - - + -
137A ALA 3.6 17.7 - - - -
140A VAL* 3.7 17.9 - - + -
204A THR 4.8 0.4 + - - -
211A ASN* 3.3 8.4 + - - +
212A LEU* 1.3 79.1 - - - +
214A LEU* 1.3 68.7 + - + +
216A ALA* 3.2 3.6 + - - +
217A VAL* 2.9 45.4 + - + +
245A ILE* 3.6 35.0 - - + -
248A PHE* 3.9 24.2 - + + -
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Residues in contact with LEU 214 (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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211A ASN* 3.0 23.1 + - + +
213A PHE* 1.3 82.4 - - + +
215A THR* 1.3 63.5 + - - +
217A VAL* 3.2 6.6 + - - +
218A HIS* 3.2 21.5 + - - +
235A VAL* 4.2 2.1 - - - +
240A TYR* 4.3 7.6 - - + +
241A LYS 3.8 11.4 - - - +
242A TYR* 3.9 12.6 - - + -
243A VAL* 3.6 32.3 - - + +
245A ILE* 3.5 24.7 - - + -
248A PHE* 3.6 34.5 - - + -
306A R4B 3.9 16.9 - - + -
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Residues in contact with THR 215 (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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181A LEU* 4.6 3.8 - - + -
182A ALA* 3.8 25.1 - - + -
197A PHE* 3.8 5.4 - - + -
203A TRP* 3.8 18.6 - - + -
210A THR* 3.4 18.7 - - - +
211A ASN 2.9 17.9 + - - -
212A LEU 3.7 3.6 - - - -
214A LEU* 1.3 77.1 - - - +
216A ALA* 1.3 57.3 + - - +
218A HIS* 3.3 3.1 + - - +
219A GLU* 2.9 27.1 + - + +
240A TYR* 3.8 7.1 - - - -
306A R4B 3.4 24.2 - - - +
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Residues in contact with ALA 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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133A ALA 4.9 0.4 - - - +
134A ILE* 3.8 26.0 - - + -
137A ALA* 3.7 17.3 - - + -
197A PHE* 3.9 17.4 - - + -
212A LEU 2.8 22.1 + - - +
213A PHE* 3.6 5.2 - - - +
215A THR* 1.3 71.3 - - - +
217A VAL* 1.3 61.0 + - - +
219A GLU 4.4 0.2 - - - +
220A ILE* 2.8 38.8 + - + +
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Residues in contact with VAL 217 (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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137A ALA* 3.8 14.4 - - + +
140A VAL* 4.0 19.3 - - + -
141A TRP* 2.8 39.8 + - + +
213A PHE* 2.9 52.9 + - + +
214A LEU* 3.2 8.9 + - - +
216A ALA* 1.3 75.2 - - - +
218A HIS* 1.3 63.3 + - - +
221A GLY 3.1 6.6 + - - -
235A VAL* 3.6 27.6 - - + -
248A PHE* 4.0 6.3 - - + -
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Residues in contact with HIS 218 (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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214A LEU 3.2 6.6 + - - +
215A THR 3.5 7.9 - - - +
217A VAL* 1.3 81.4 - - - +
219A GLU* 1.3 71.7 + - - +
221A GLY 3.1 9.4 + - - -
222A HIS* 3.2 10.7 + + - -
228A HIS* 3.6 9.9 - + - -
235A VAL* 2.7 26.2 + - + +
236A MET* 3.4 26.4 - - + +
237A PHE 3.2 22.7 - - - -
238A PRO 4.5 0.7 - - - -
301A ZN 2.0 37.0 - - - -
306A R4B 3.3 42.8 + + + +
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Residues in contact with GLU 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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182A ALA* 3.3 21.6 - - + +
183A HIS* 3.1 31.8 - - - +
184A ALA* 3.1 13.8 + - + +
195A ALA* 4.3 4.9 - - + -
196A HIS 5.0 0.2 - - - +
197A PHE* 4.2 17.0 - - + -
215A THR* 2.9 20.5 + - + +
216A ALA 3.4 2.7 + - - +
218A HIS* 1.3 77.6 - - - +
220A ILE* 1.3 59.0 + - + +
222A HIS* 3.0 11.1 + - - +
223A SER* 2.8 29.0 + - - -
306A R4B 2.7 45.2 + - - +
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Residues in contact with ILE 220 (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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134A ILE* 4.4 3.1 - - + +
137A ALA* 3.6 24.7 - - + -
138A PHE* 3.7 58.1 - - + +
141A TRP* 3.6 21.5 - - + -
159A ILE* 5.7 0.7 - - + -
161A VAL* 6.2 2.5 - - + -
195A ALA* 5.5 6.1 - - + -
197A PHE* 6.2 0.9 - - + -
216A ALA* 2.8 32.1 + - + +
219A GLU* 1.3 69.8 - - + +
221A GLY* 1.3 66.2 + - - +
223A SER* 3.0 11.4 + - - +
224A LEU* 2.9 34.7 + - + +
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Residues in contact with GLY 221 (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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141A TRP* 3.6 24.6 - - - +
217A VAL 3.1 11.5 + - - -
218A HIS 3.1 6.4 + - - -
220A ILE* 1.3 76.4 - - - +
222A HIS* 1.3 59.2 + - - +
224A LEU* 3.2 11.0 + - - +
225A GLY 3.2 0.5 + - - -
226A LEU* 2.9 35.9 + - - +
236A MET* 3.9 5.6 - - - -
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Residues in contact with HIS 222 (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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184A ALA* 3.9 20.2 - - + +
185A PHE 4.3 1.8 - - - -
186A GLY* 3.6 13.4 - - - -
218A HIS* 3.2 13.9 + + - -
219A GLU* 3.0 18.4 + - - +
221A GLY* 1.3 76.5 - - - +
223A SER* 1.3 57.6 + - - +
225A GLY* 2.9 19.6 + - - -
226A LEU 2.9 25.8 + - - +
227A GLY* 4.3 5.6 - - - -
228A HIS* 3.4 18.8 - + - -
236A MET* 3.5 9.2 - - + +
301A ZN 2.1 38.0 - - - -
306A R4B 3.5 19.6 + + - -
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Residues in contact with SER 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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109A TRP* 2.8 24.3 + - - -
159A ILE* 4.0 18.0 - - - +
184A ALA* 3.7 9.9 - - - +
185A PHE 3.5 10.3 - - - -
187A PRO* 3.4 12.3 - - - +
193A GLY* 2.8 25.6 + - - -
195A ALA* 4.0 7.8 - - - +
219A GLU 2.8 19.0 + - - -
220A ILE* 3.0 15.7 + - - +
222A HIS* 1.3 72.2 - - - +
224A LEU* 1.3 58.1 + - - +
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Residues in contact with LEU 224 (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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107A PRO 4.4 0.7 - - - +
109A TRP* 3.8 23.3 - - + +
114A ILE* 4.2 1.1 - - + -
141A TRP* 3.9 33.2 - - + -
147A LEU* 4.0 16.8 - - + -
149A PHE* 4.0 25.6 - - + -
159A ILE* 4.6 6.1 - - + -
187A PRO* 3.5 5.8 - - - +
220A ILE* 2.9 27.3 + - + +
221A GLY* 3.7 5.2 - - - +
222A HIS 3.0 0.4 - - - -
223A SER* 1.3 78.5 - - - +
225A GLY* 1.3 58.0 + - - +
226A LEU 3.7 0.4 - - - -
258A ILE* 3.9 22.4 - - + -
261A LEU* 3.8 4.5 - - - +
262A TYR* 2.7 30.4 + - + -
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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
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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