Contacts of the helix formed by residues 212 - 227 (chain A) in PDB entry 2EIT
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 ALA 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLU* 3.4 9.4 - - - -
124A VAL* 3.9 8.7 - - + -
183A TRP* 4.1 10.5 - - - -
186A PRO* 3.3 38.0 - - + +
208A PRO* 4.4 3.9 - - + +
209A ALA* 2.9 12.7 + - + +
211A ASP* 1.3 78.9 - - - +
213A VAL* 1.3 63.9 + - - +
214A VAL 3.3 2.9 - - - -
215A VAL* 3.6 4.5 - - + +
216A GLY* 3.3 18.9 + - - -
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Residues in contact with VAL 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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53A MET* 4.6 15.5 - - + +
54A VAL 5.1 0.7 - - - -
55A SER* 3.9 20.6 - - - +
67A THR 5.6 0.2 - - - -
68A THR* 3.7 26.3 - - + +
123A GLU* 3.2 0.6 + - - -
208A PRO* 4.0 12.3 - - + +
209A ALA 3.5 14.6 - - - +
210A GLU* 3.5 22.2 - - - +
212A ALA* 1.3 76.1 - - - +
214A VAL* 1.3 62.6 + - + +
216A GLY 3.5 0.3 + - - -
217A ALA* 3.0 23.7 + - - +
235A PHE* 3.3 9.9 - - - -
237A PRO* 3.7 25.1 - - + -
238A GLY 5.1 0.2 - - - +
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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
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38A TYR* 3.5 34.0 - - + +
55A SER* 3.8 12.1 - - - -
65A VAL* 4.4 11.2 - - + +
66A GLY* 3.8 32.1 - - - +
68A THR* 4.6 3.6 - - + -
119A THR* 4.2 15.7 - - + -
123A GLU* 2.9 20.6 + - - +
213A VAL* 1.3 78.8 - - + +
215A VAL* 1.3 67.2 + - - +
217A ALA* 3.0 16.9 + - - +
218A LYS* 3.1 15.6 + - - +
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Residues in contact with VAL 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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116A LEU* 4.3 13.5 - - + +
119A THR* 3.8 28.9 - - + -
120A LEU* 4.2 10.1 - - + -
123A GLU* 2.8 23.4 + - + +
124A VAL* 5.9 0.4 - - + -
186A PRO* 3.8 35.4 - - + +
187A VAL* 3.3 24.7 - - + -
212A ALA 3.6 8.5 - - - +
214A VAL* 1.3 73.4 - - - +
216A GLY* 1.3 64.2 - - - +
218A LYS* 3.1 4.3 + - + +
219A VAL* 3.0 24.4 + - - +
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Residues in contact with GLY 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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186A PRO 4.7 2.0 - - - -
190A PHE* 3.9 23.8 - - - -
208A PRO* 4.9 1.6 - - - -
212A ALA 3.3 9.7 + - - -
213A VAL 3.8 3.6 - - - -
214A VAL 3.2 0.8 - - - -
215A VAL* 1.3 83.3 - - - +
217A ALA* 1.3 62.1 + - - +
219A VAL* 3.2 5.4 + - - +
220A PHE* 3.1 25.5 + - - -
235A PHE* 3.6 13.2 - - - -
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Residues in contact with ALA 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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38A TYR* 3.6 38.4 - - + -
46A TRP* 3.7 6.3 - - + -
213A VAL 3.0 13.5 + - - +
214A VAL 3.3 9.4 - - - +
216A GLY* 1.3 75.9 - - - +
218A LYS* 1.3 57.4 + - - +
220A PHE* 3.0 6.1 + - - +
221A GLU* 2.9 29.3 + - - +
235A PHE* 3.3 20.8 - - + -
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A VAL* 4.1 3.2 - - - +
33A GLU* 2.8 30.6 + - - -
36A ARG* 4.6 1.8 - - - +
38A TYR* 3.6 22.4 - - + -
112A ARG* 3.7 3.9 + - - +
115A GLU* 2.9 31.4 + - - +
116A LEU* 3.8 19.5 - - + -
119A THR* 3.0 41.4 + - + +
214A VAL* 3.1 12.6 + - - +
215A VAL 3.1 6.9 + - - +
217A ALA* 1.3 73.4 - - - +
219A VAL* 1.3 65.8 + - - +
221A GLU* 3.1 31.4 + - - +
222A ILE* 3.2 16.8 + - - +
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Residues in contact with VAL 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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109A MET* 4.3 11.0 - - + -
116A LEU* 4.9 4.3 - - + -
187A VAL* 4.0 31.6 - - + -
190A PHE* 4.0 18.2 - - + -
191A THR* 3.7 15.0 - - - +
215A VAL 3.0 18.1 + - - +
216A GLY 3.2 7.8 + - - +
218A LYS* 1.3 76.3 - - - +
220A PHE* 1.3 57.1 + - - +
222A ILE* 3.0 12.2 + - - +
223A PHE* 3.0 54.8 + - + -
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Residues in contact with PHE 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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41A TYR* 3.7 17.6 - + - -
46A TRP* 3.9 16.3 - - + -
190A PHE* 3.5 26.2 - + - -
194A ILE* 3.9 8.7 - - + -
206A ALA* 4.0 7.6 - - + -
216A GLY 3.1 11.7 + - - +
217A ALA 3.0 9.6 + - - +
219A VAL* 1.3 75.0 - - - +
221A GLU* 1.3 58.8 + - - +
223A PHE* 3.2 16.3 + + + +
224A HIS* 2.9 30.5 + - - +
233A VAL* 3.6 24.2 - - + -
234A ASN 3.3 43.5 - - - -
235A PHE* 3.6 31.9 - + + -
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Residues in contact with GLU 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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36A ARG* 2.6 35.9 + - - -
38A TYR* 4.7 4.8 - - + -
46A TRP* 4.0 19.5 - - + +
112A ARG* 2.8 39.6 + - - +
217A ALA 2.9 16.8 + - - +
218A LYS* 3.1 20.0 + - - +
220A PHE* 1.3 74.1 - - - +
222A ILE* 1.3 58.1 + - - +
224A HIS* 3.3 6.6 + - - +
225A GLU* 2.9 30.5 + - - +
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Residues in contact with ILE 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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105A ALA* 3.6 32.3 - - + +
108A LEU* 3.9 13.4 - - + +
109A MET* 3.8 36.8 - - + +
112A ARG* 3.8 26.2 - - - +
116A LEU* 3.8 24.5 - - + -
218A LYS 3.2 12.8 + - - +
219A VAL* 3.0 10.6 + - - +
221A GLU* 1.3 75.0 - - - +
223A PHE* 1.3 69.3 + - + +
225A GLU* 3.3 6.7 + - - +
226A ALA* 2.9 22.7 + - - +
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Residues in contact with PHE 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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41A TYR* 5.9 0.4 - - + -
105A ALA* 4.6 11.0 - - + -
109A MET* 5.4 0.4 - - + -
142A ILE* 5.2 3.1 - - + -
191A THR* 4.6 9.0 - - + -
194A ILE* 4.0 31.6 - - + -
195A VAL* 3.9 30.3 - - + -
219A VAL* 3.0 42.9 + - + -
220A PHE* 3.6 22.9 - + + +
222A ILE* 1.3 79.7 - - + +
224A HIS* 1.3 63.3 + - - +
226A ALA* 3.3 1.3 + - - -
227A GLY 3.1 16.5 + - - -
228A PHE* 3.5 40.4 + + + +
233A VAL* 3.9 27.4 - - + -
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Residues in contact with HIS 224 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A TYR* 2.7 45.2 + + + +
44A GLY 3.9 13.5 - - - -
46A TRP* 4.4 15.9 + + - +
220A PHE 2.9 17.6 + - - +
221A GLU* 3.6 7.9 - - - +
223A PHE* 1.3 76.0 - - - +
225A GLU* 1.3 67.7 + - + +
227A GLY* 3.1 14.4 + - - -
228A PHE 5.3 1.3 - - - +
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LYS* 5.7 0.3 - - - +
108A LEU* 3.8 29.6 - - + +
112A ARG* 5.6 7.8 + - - -
221A GLU 2.9 17.4 + - - +
222A ILE* 3.8 5.6 - - - +
224A HIS* 1.3 81.4 - - + +
226A ALA* 1.3 62.4 + - - +
227A GLY* 3.3 1.0 + - - -
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Residues in contact with ALA 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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101A LEU* 3.5 25.8 - - + +
104A LYS* 3.9 18.4 - - + +
105A ALA* 4.0 18.4 - - + -
108A LEU* 3.5 16.5 - - + +
222A ILE 2.9 16.8 + - - +
223A PHE 3.5 6.1 - - - +
224A HIS 3.2 0.2 - - - -
225A GLU* 1.3 77.5 - - - +
227A GLY* 1.3 58.3 + - - +
228A PHE* 4.3 2.2 - - + -
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Residues in contact with GLY 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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93A TRP* 5.4 1.4 - - - -
101A LEU* 4.0 8.0 - - - +
223A PHE 3.1 1.4 + - - -
224A HIS 3.1 15.6 + - - -
225A GLU 3.2 1.3 - - - -
226A ALA* 1.3 80.1 - - - +
228A PHE* 1.3 69.4 + - - +
229A PRO* 3.2 8.5 - - - +
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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