Contacts of the helix formed by residues 187 - 200 (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 VAL 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B MET* 4.4 8.1 - - + -
116B LEU* 4.6 8.3 - - + -
120B LEU* 3.8 17.7 - - + -
134B ASP* 3.4 8.9 + - - +
135B VAL* 4.3 15.7 - - + -
138B ALA* 3.6 19.5 - - + -
185B PHE 3.3 0.2 - - - -
186B PRO* 1.3 83.6 - - - +
188B ALA* 1.3 59.4 + - - +
189B ILE 3.6 0.2 - - - -
190B PHE* 3.9 0.4 - - - +
191B THR* 2.8 37.8 + - - +
215B VAL* 3.4 33.7 - - + -
219B VAL* 4.0 21.1 - - + -
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ASP* 2.8 35.0 + - - +
137B GLU* 3.7 32.5 - - + +
138B ALA* 3.6 11.4 - - - +
141B PHE* 3.2 12.1 - - - -
185B PHE* 3.6 7.8 + - + -
187B VAL* 1.3 74.0 - - - +
189B ILE* 1.3 59.8 + - - +
191B THR* 3.7 1.4 - - - -
192B GLY 2.9 24.1 + - - -
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLU* 4.5 11.9 - - - +
141B PHE* 4.5 8.3 - - + -
182B PRO* 3.7 23.3 - - + -
185B PHE* 3.0 35.4 + - + +
188B ALA* 1.3 74.6 - - - +
190B PHE* 1.3 65.6 + - - +
192B GLY 4.4 0.4 - - - +
193B MET* 3.0 34.5 + - + +
259B THR* 3.9 19.1 - - + +
485B PHE* 6.0 0.9 - - + -
2517B ALA* 4.7 8.1 - - + +
2518B NAD 3.5 39.3 - - + +
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Residues in contact with PHE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 4.6 0.8 - - + +
181B ALA* 3.6 29.7 - - + +
182B PRO* 4.9 0.2 - - - +
185B PHE 3.5 3.2 + - - -
186B PRO* 3.2 31.2 - - + +
187B VAL 3.9 0.2 - - - +
189B ILE* 1.3 80.7 - - - +
191B THR* 1.3 62.6 + - - +
193B MET* 3.7 2.1 + - - +
194B ILE* 3.1 39.1 + - + +
206B ALA* 4.0 16.8 - - + -
207B LYS 4.6 0.2 - - - -
208B PRO* 3.8 26.5 - - + -
216B GLY* 3.7 23.8 - - - -
219B VAL* 4.0 19.3 - - + -
220B PHE* 3.5 28.7 - + - -
235B PHE* 4.1 10.5 - + - -
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Residues in contact with THR 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B MET* 3.8 10.5 - - + +
138B ALA* 3.8 12.6 - - - +
142B ILE* 3.5 38.6 - - + -
187B VAL 2.8 25.5 + - - -
188B ALA 3.7 2.5 - - - -
190B PHE* 1.3 79.5 - - - +
192B GLY* 1.3 56.7 + - - +
194B ILE* 3.2 5.6 + - - +
195B VAL* 2.8 38.3 + - + +
219B VAL* 3.7 20.4 - - - +
223B PHE* 4.6 5.8 - - + -
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Residues in contact with GLY 192 (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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141B PHE* 3.6 36.7 - - - -
145B TYR* 3.5 11.4 - - - -
188B ALA 2.9 14.5 + - - -
189B ILE* 3.9 0.9 - - - -
191B THR* 1.3 72.5 - - - +
193B MET* 1.3 62.2 + - - +
195B VAL* 4.3 1.1 - - - -
196B GLY* 3.1 22.3 + - - -
502B TYR* 4.1 4.8 - - - -
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Residues in contact with MET 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 3.2 25.4 - - + +
180B ILE 3.2 28.5 - - - +
181B ALA* 3.7 19.1 - - + -
189B ILE* 3.0 24.0 + - + +
190B PHE 4.2 0.2 - - - +
192B GLY* 1.3 75.8 - - - +
194B ILE* 1.3 57.0 + - - +
197B PRO* 3.1 18.5 - - - +
257B ASN* 3.1 50.0 + - - +
258B PHE 3.9 1.8 - - - +
259B THR* 3.2 29.8 - - - +
497B THR* 5.9 3.6 - - + -
502B TYR* 3.7 9.9 - - - +
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 4.0 13.9 - - + -
190B PHE* 3.1 43.9 + - + +
191B THR 3.2 4.3 + - - +
193B MET* 1.3 78.1 - - - +
195B VAL* 1.3 68.2 + - + +
196B GLY 3.3 0.2 - - - -
197B PRO* 3.4 5.2 - - - +
198B VAL* 3.2 22.5 + - + +
204B VAL* 4.1 11.9 - - + +
206B ALA* 3.6 31.6 - - + -
220B PHE* 3.9 7.9 - - + -
223B PHE* 4.0 16.4 - - + -
233B VAL* 3.7 30.1 - - + -
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 3.8 19.7 - - + +
105B ALA* 6.1 0.7 - - + -
142B ILE* 4.0 30.1 - - + +
145B TYR* 4.0 16.8 - - + -
191B THR* 2.8 32.8 + - + +
192B GLY* 4.3 1.3 - - - -
194B ILE* 1.3 72.8 - - + +
196B GLY* 1.3 62.4 + - - +
198B VAL* 3.8 6.5 - - + -
199B ALA* 2.9 32.1 + - - +
223B PHE* 3.9 31.6 - - + -
228B PHE* 5.2 7.6 - - + -
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Residues in contact with GLY 196 (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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145B TYR* 3.6 22.0 - - - -
192B GLY 3.1 11.7 + - - -
195B VAL* 1.3 80.8 - - - +
197B PRO* 1.3 68.8 - - - +
199B ALA* 3.3 8.8 + - - +
200B VAL* 3.8 4.9 + - - +
502B TYR* 4.5 2.9 - - - -
503B LEU* 3.4 27.3 - - - +
506B PHE* 4.8 1.3 - - - -
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Residues in contact with PRO 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 5.2 0.2 - - + -
192B GLY 4.2 1.1 - - - +
193B MET 3.1 29.2 - - - +
194B ILE 3.4 4.9 - - - +
196B GLY* 1.3 87.1 - - - +
198B VAL* 1.3 61.2 + - - +
199B ALA 3.4 0.5 + - - -
200B VAL* 3.4 5.2 + - - +
202B ASN* 3.0 34.2 + - + +
204B VAL* 4.1 5.8 - - + -
255B PHE* 3.9 27.4 - - + -
257B ASN* 4.1 2.2 - - - +
502B TYR* 4.7 0.9 - - + -
506B PHE* 3.6 43.5 - - + -
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Residues in contact with VAL 198 (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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90B TRP* 3.0 36.8 + - + -
102B LEU* 4.7 2.0 - - + -
194B ILE* 3.2 19.0 + - + +
195B VAL* 4.0 6.7 - - + +
196B GLY 3.3 0.4 - - - -
197B PRO* 1.3 75.1 - - - +
199B ALA* 1.3 67.0 + - - +
201B GLY 3.0 4.3 + - - -
202B ASN 3.4 15.7 - - - +
204B VAL* 3.9 16.2 - - + -
228B PHE* 3.7 30.3 - - + -
232B VAL* 3.8 13.0 - - + +
233B VAL* 3.8 23.8 - - + -
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Residues in contact with ALA 199 (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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95B GLN* 2.9 24.7 + - - +
98B ARG* 3.0 15.0 + - - +
99B SER* 5.7 0.2 - - - +
102B LEU* 3.8 29.2 - - + -
145B TYR* 4.2 8.1 - - + +
146B ALA* 5.2 0.7 - - - -
149B ALA* 4.1 17.7 - - + -
195B VAL 2.9 19.5 + - - +
196B GLY 3.5 7.0 - - - +
197B PRO 3.3 0.2 - - - -
198B VAL* 1.3 76.7 - - - +
200B VAL* 1.3 58.8 + - + +
503B LEU* 5.0 0.4 - - + -
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Residues in contact with VAL 200 (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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95B GLN* 3.7 8.3 - - - +
98B ARG* 3.5 12.9 + - - -
149B ALA* 3.9 27.4 - - + +
152B TYR* 5.1 2.7 - - + -
173B PRO* 3.5 17.7 - - - +
196B GLY 4.0 6.7 - - - +
197B PRO 3.4 13.7 - - - +
199B ALA* 1.3 76.3 - - - +
201B GLY* 1.3 56.8 + - - +
202B ASN* 3.5 13.5 - - - +
503B LEU* 4.0 25.8 - - + +
506B PHE* 4.0 9.0 - - + +
507B LEU* 3.8 33.0 - - + +
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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