Contacts of the helix formed by residues 212 - 227 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B GLU* 3.5 8.5 - - - -
124B VAL* 3.9 8.7 - - + -
183B TRP* 4.3 10.3 - - - -
186B PRO* 3.3 38.1 - - + +
208B PRO* 4.4 4.6 - - + +
209B ALA* 3.0 12.6 + - + +
211B ASP* 1.3 80.3 - - - +
213B VAL* 1.3 63.8 + - - +
214B VAL 3.4 2.7 - - - -
215B VAL* 3.6 3.8 - - + +
216B GLY* 3.3 18.4 + - - -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B MET* 4.6 16.4 - - + -
54B VAL 5.2 0.2 - - - -
55B SER* 4.1 20.2 - - - +
67B THR 5.6 0.2 - - - -
68B THR* 3.6 30.5 - - + +
123B GLU* 3.3 0.6 + - - -
208B PRO* 4.1 12.1 - - + +
209B ALA 3.5 15.0 - - - +
210B GLU* 3.6 20.9 - - - +
212B ALA* 1.3 75.9 - - - +
214B VAL* 1.3 63.2 + - + +
216B GLY 3.5 0.2 + - - -
217B ALA* 3.0 24.1 + - - +
235B PHE* 3.4 9.9 - - - -
237B PRO* 3.8 24.5 - - + -
238B GLY 5.1 0.2 - - - +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 3.6 33.4 - - + +
55B SER* 3.8 17.7 - - - -
65B VAL* 4.3 10.8 - - + +
66B GLY* 3.8 25.4 - - - +
67B THR 4.5 0.2 - - - +
68B THR* 4.6 2.5 - - + -
119B THR* 4.1 8.7 - - + -
123B GLU* 2.9 19.3 + - + +
213B VAL* 1.3 78.5 - - + +
215B VAL* 1.3 66.2 + - - +
217B ALA* 3.1 16.6 + - - +
218B LYS* 3.1 25.6 + - - +
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.3 13.0 - - + +
119B THR* 3.8 28.3 - - + -
120B LEU* 4.1 10.5 - - + -
123B GLU* 2.8 24.2 + - + +
186B PRO* 3.8 35.7 - - + +
187B VAL* 3.4 24.0 - - + -
212B ALA* 3.6 9.0 - - + +
214B VAL* 1.3 73.4 - - - +
216B GLY* 1.3 65.6 + - - +
218B LYS* 3.2 4.2 + - - +
219B VAL* 3.0 23.5 + - - +
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Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PRO 4.6 2.2 - - - -
190B PHE* 3.7 23.7 - - - -
208B PRO* 4.9 1.8 - - - -
212B ALA 3.3 9.6 + - - -
213B VAL 3.8 3.6 - - - -
214B VAL 3.2 0.6 - - - -
215B VAL* 1.3 84.6 - - - +
217B ALA* 1.3 59.7 + - - +
219B VAL* 3.2 5.9 + - - +
220B PHE* 3.1 25.3 + - - -
235B PHE* 3.6 12.6 - - - -
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B TYR* 3.6 37.0 - - + -
46B TRP* 3.6 6.1 - - + -
68B THR* 4.9 0.2 - - + -
213B VAL 3.0 14.2 + - - +
214B VAL 3.1 9.4 + - - +
216B GLY* 1.3 76.3 - - - +
218B LYS* 1.3 57.6 + - - +
220B PHE* 3.1 5.9 + - - +
221B GLU* 2.9 30.4 + - - +
235B PHE* 3.4 21.0 - - + -
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Residues in contact with LYS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 4.0 22.4 + - - +
33B GLU* 4.6 7.2 + - - +
36B ARG* 4.6 5.6 - - - +
38B TYR* 3.4 29.7 + - + -
112B ARG* 3.7 7.8 + - - +
115B GLU* 3.8 20.4 + - - +
116B LEU* 3.9 18.2 - - + -
119B THR* 2.7 44.8 + - + +
214B VAL* 3.1 15.4 + - - +
215B VAL 3.2 7.6 + - - +
217B ALA* 1.3 73.5 - - - +
219B VAL* 1.3 66.4 + - - +
221B GLU* 3.2 30.1 + - - +
222B ILE* 3.3 12.3 + - - +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B MET* 4.2 10.1 - - + -
116B LEU* 4.8 5.2 - - + -
187B VAL* 4.0 31.6 - - + -
190B PHE* 4.0 17.9 - - + -
191B THR* 3.7 15.3 - - - +
215B VAL 3.0 17.6 + - - +
216B GLY 3.2 8.2 + - - +
218B LYS* 1.3 76.8 - - - +
220B PHE* 1.3 55.8 + - - +
222B ILE* 3.1 13.9 + - - +
223B PHE* 3.0 53.8 + - + -
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Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TYR* 3.8 17.1 - + + -
46B TRP* 4.0 16.1 - - + -
190B PHE* 3.5 27.1 - + - -
194B ILE* 3.9 4.3 - - + -
204B VAL* 6.2 0.2 - - + -
206B ALA* 4.1 6.3 - - + -
216B GLY 3.1 13.0 + - - +
217B ALA 3.1 8.7 + - - +
219B VAL* 1.3 73.5 - - - +
221B GLU* 1.3 58.7 + - - +
223B PHE* 3.7 23.7 - + + +
224B HIS* 2.8 31.4 + - - +
233B VAL* 3.6 22.0 - - + -
234B ASN 3.4 44.4 - - - -
235B PHE* 3.6 30.7 - + + -
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 2.7 36.1 + - - -
38B TYR* 4.8 1.6 - - - -
46B TRP* 3.9 19.9 - - + +
112B ARG* 2.8 37.7 + - - +
115B GLU* 4.6 0.5 - - - +
217B ALA 2.9 17.1 + - - +
218B LYS* 3.2 22.1 + - - +
220B PHE* 1.3 75.8 - - - +
222B ILE* 1.3 56.4 + - - +
224B HIS* 3.4 5.1 + - - +
225B GLU* 2.9 30.3 + - - +
2531B MPD 3.4 17.2 - - + +
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ALA* 3.6 32.8 - - + +
108B LEU* 3.8 14.2 - - + +
109B MET* 3.9 30.5 - - + +
112B ARG* 3.9 27.8 - - - +
116B LEU* 3.8 29.8 - - + -
218B LYS 3.3 12.5 + - - +
219B VAL* 3.1 10.8 + - - +
221B GLU* 1.3 74.4 - - - +
223B PHE* 1.3 63.5 - - + +
225B GLU* 3.2 4.3 + - - -
226B ALA* 2.9 28.6 + - - +
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Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 5.8 0.9 - - + -
105B ALA* 4.6 10.8 - - + -
109B MET* 5.4 0.7 - - + -
142B ILE* 5.2 2.9 - - + -
191B THR* 4.6 9.9 - - + -
194B ILE* 4.0 21.3 - - + -
195B VAL* 3.9 30.3 - - + -
219B VAL* 3.0 37.9 + - + -
220B PHE* 3.7 46.4 - + + +
222B ILE* 1.3 77.8 - - + +
224B HIS* 1.3 62.3 + - - +
226B ALA* 3.3 1.1 + - - -
227B GLY 3.2 17.0 + - - -
228B PHE* 3.5 42.1 + + + +
233B VAL* 3.9 17.7 - - + -
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Residues in contact with HIS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TYR* 2.6 45.4 + + + +
44B GLY 3.8 14.1 - - - -
45B GLU* 5.6 0.2 - - - -
46B TRP* 4.4 16.6 + + - +
220B PHE 2.8 21.0 + - - +
221B GLU* 3.6 7.6 - - - +
223B PHE* 1.3 74.2 - - - +
225B GLU* 1.3 67.4 + - + +
227B GLY* 3.1 15.1 + - - -
228B PHE 5.4 1.5 - - - +
2531B MPD 6.4 0.2 - - + -
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Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LYS* 5.7 0.5 - - - +
108B LEU* 3.7 30.0 - - + +
112B ARG* 4.6 14.7 + - - -
221B GLU 2.9 17.3 + - - +
222B ILE* 3.2 4.6 + - - +
224B HIS* 1.3 83.3 - - + +
226B ALA* 1.3 62.4 + - - +
227B GLY* 3.4 1.4 + - - -
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Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 3.5 24.2 - - + +
104B LYS* 3.8 21.6 - - + +
105B ALA* 4.0 17.7 - - + -
108B LEU* 3.5 16.3 - - + +
222B ILE 2.9 17.0 + - - +
223B PHE 3.6 6.3 - - - +
224B HIS 3.2 0.2 - - - -
225B GLU* 1.3 77.7 - - - +
227B GLY* 1.3 57.6 + - - +
228B PHE* 3.7 1.8 - - + -
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Residues in contact with GLY 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B TRP* 5.4 1.6 - - - -
101B LEU* 4.0 8.2 - - - +
223B PHE 3.2 1.2 + - - -
224B HIS 3.1 15.2 + - - -
225B GLU 3.2 1.5 - - - -
226B ALA* 1.3 79.2 - - - +
228B PHE* 1.3 69.9 + - - +
229B 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
------------------------------------------------------------
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