Contacts of the helix formed by residues 198 - 214 (chain B) in PDB entry 4IA4
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 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ALA* 3.2 19.3 + - + +
196B ILE 4.2 0.2 + - - -
197B LEU* 1.3 69.9 - - - +
199B PRO* 1.3 69.6 - - + +
201B PRO* 3.8 14.3 - - + +
202B ILE* 3.2 26.3 - - - +
90D TYR* 3.2 27.4 - - + +
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Residues in contact with PRO 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE 5.1 0.2 - - - +
86B PHE* 3.4 39.1 - - + +
89B VAL* 4.1 11.7 - - + -
90B TYR* 3.8 37.5 - - + +
197B LEU 3.3 6.0 - - - +
198B ALA* 1.3 84.9 - - + +
200B LEU* 1.3 66.1 + - + +
201B PRO* 4.8 0.4 - - + -
202B ILE* 3.3 4.6 + - + +
203B GLY* 2.9 25.3 + - - -
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 3.2 35.5 - - + -
199B PRO* 1.3 82.3 - - + +
201B PRO* 1.3 65.1 - - + +
203B GLY* 3.1 1.2 + - - -
204B PHE* 2.8 50.7 + - + +
200C LEU* 4.9 13.9 - - + -
204C PHE* 5.6 6.1 - - + -
86D PHE* 3.9 23.6 - - + -
200D LEU* 4.5 19.7 - - + -
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Residues in contact with PRO 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 3.4 12.6 - - + +
198B ALA* 3.8 15.7 - - + -
199B PRO* 3.7 2.7 - - + -
200B LEU* 1.3 95.1 - - + +
202B ILE* 1.3 56.9 + - + +
205B ALA* 3.1 25.6 + - - +
86D PHE* 4.2 19.7 - - + -
87D VAL* 3.9 8.2 - - + +
90D TYR* 3.5 58.1 - - + +
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Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 3.4 23.3 - - + -
89B VAL* 4.6 10.5 - - + -
175B LEU* 4.2 15.2 - - + +
178B THR* 4.3 5.8 - - + -
179B VAL* 3.9 29.2 - - + +
182B ALA* 4.0 15.3 - - + -
197B LEU* 3.8 27.6 - - + -
198B ALA 3.2 20.4 - - - +
199B PRO* 3.3 8.4 + - + +
200B LEU 3.1 0.4 - - - -
201B PRO* 1.3 75.6 - - - +
203B GLY* 1.3 66.3 + - - +
205B ALA* 3.1 7.1 + - - +
206B VAL* 3.0 21.3 + - - +
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Residues in contact with GLY 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY* 3.2 30.4 - - - -
85B ILE* 3.9 10.5 - - - -
86B PHE* 3.9 8.5 - - - -
199B PRO 2.9 15.6 + - - -
200B LEU 3.1 2.4 + - - -
202B ILE* 1.3 77.2 - - - +
204B PHE* 1.3 56.5 + - - +
206B VAL 3.0 2.9 + - - -
207B PHE* 2.8 25.2 + - - +
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Residues in contact with PHE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TRP* 4.0 23.6 - + - -
200B LEU* 2.8 40.5 + - + +
201B PRO 4.0 0.4 - - - +
203B GLY* 1.3 76.3 - - - +
205B ALA* 1.3 53.4 + - - +
207B PHE* 3.2 8.5 + + - +
208B MET* 2.7 69.1 + - + +
204C PHE* 5.5 4.0 - + - -
79D TRP* 4.0 28.5 - + - -
83D GLY* 4.0 9.4 - - - -
86D PHE* 3.7 27.4 - + + -
87D VAL* 3.6 16.4 - - + -
200D LEU* 5.7 4.0 - - + -
204D PHE* 5.3 7.4 - + - -
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 4.3 12.3 - - + +
175B LEU* 4.3 12.3 - - + -
178B THR* 3.9 21.1 - - - +
201B PRO 3.1 15.3 + - - +
202B ILE* 3.1 12.4 + - - +
204B PHE* 1.3 73.2 - - - +
206B VAL* 1.3 66.4 + - - +
208B MET* 3.3 4.1 + - - +
209B VAL* 3.0 31.2 + - - +
87D VAL* 3.9 9.4 - - + +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 5.4 1.8 - - + -
81B PHE* 3.7 6.3 - - + -
82B GLY* 3.5 22.9 - - - +
85B ILE* 3.4 29.4 - - + -
175B LEU* 3.8 26.5 - - + -
202B ILE 3.0 16.2 + - - +
203B GLY 3.4 6.7 - - - +
205B ALA* 1.3 74.6 - - - +
207B PHE* 1.3 62.7 + - - +
209B VAL* 3.6 1.8 + - - +
210B HIS* 2.9 45.8 + - + +
219B THR* 4.3 0.2 - - - +
221B ILE* 4.2 14.1 - - + -
222B ASN* 6.2 1.3 - - - +
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Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.9 13.2 - - + -
78B ALA* 3.4 42.6 - - + -
79B TRP* 3.5 62.6 - + + -
82B GLY* 3.5 11.1 - - - -
203B GLY 2.8 12.8 + - - +
204B PHE* 3.2 14.6 - + + +
206B VAL* 1.3 76.1 - - - +
208B MET* 1.3 95.8 + - + +
210B HIS* 2.9 15.6 + - - +
211B LEU* 3.1 18.1 + - + +
79D TRP* 3.9 17.5 - + + -
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Residues in contact with MET 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 5.5 0.4 - - + -
204B PHE* 2.7 35.3 + - + +
205B ALA* 3.7 5.2 - - - +
207B PHE* 1.3 104.9 - - + +
209B VAL* 1.3 67.1 + - + +
211B LEU* 3.0 23.5 + - - +
212B ALA 3.4 4.0 + - - -
54D ILE* 3.9 9.7 - - + +
79D TRP* 3.8 11.4 - - + +
80D ALA* 3.8 14.4 - - - +
83D GLY* 3.1 29.8 - - - +
84D MET* 3.5 49.1 - - + +
87D VAL* 4.4 3.1 - - + -
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLY* 3.7 24.0 - - - +
174B VAL* 3.6 30.3 - - + -
175B LEU* 4.7 3.6 - - + +
205B ALA 3.0 17.8 + - - +
206B VAL* 3.9 4.3 - - - +
208B MET* 1.3 75.3 - - - +
210B HIS* 1.3 57.1 + - - +
212B ALA* 3.3 2.3 + - - +
213B THR* 2.9 34.3 + - - +
219B THR* 3.8 4.7 - - + -
221B ILE* 3.5 35.4 - - + -
54D ILE* 4.1 11.9 - - + +
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Residues in contact with HIS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA* 4.2 15.0 - - + -
81B PHE* 3.2 53.0 - + + +
82B GLY 4.6 0.2 - - - -
206B VAL* 2.9 37.9 + - + +
207B PHE* 2.9 9.9 + - - +
209B VAL* 1.3 71.0 - - - +
211B LEU* 1.3 67.7 + - - +
212B ALA 2.9 3.6 + - - -
214B ILE* 3.1 28.2 + - + +
218B GLY 3.5 8.9 + - - -
219B THR* 2.5 64.9 + - + +
221B ILE* 4.1 3.8 - - + +
225B ARG* 5.3 0.7 - - - -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.5 29.6 - - + -
78B ALA* 3.6 16.2 - - + -
207B PHE* 3.1 23.9 + - + +
208B MET* 3.0 15.7 + - - +
210B HIS* 1.3 77.8 - - - +
212B ALA* 1.3 59.7 + - - +
214B ILE* 5.7 0.2 - - - -
215B PRO* 4.5 7.6 - - - +
58D THR* 3.1 25.4 + - + +
72D VAL* 4.2 27.3 - - + +
76D GLY 3.6 9.9 - - - +
79D TRP* 3.8 10.8 - - + -
80D ALA* 3.5 35.0 - - + +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B MET 3.4 0.8 + - - -
209B VAL 3.3 2.7 + - - +
210B HIS 3.0 0.8 - - - -
211B LEU* 1.3 80.7 - - - +
213B THR* 1.3 61.3 + - - +
214B ILE 3.8 0.2 - - - -
215B PRO* 3.8 9.9 - - - +
216B ILE* 4.0 13.0 - - - +
53D TYR* 5.6 1.7 + - + -
54D ILE* 3.4 41.5 - - + +
57D ALA* 4.1 18.3 - - + +
58D THR* 3.0 23.1 + - - +
141D MET* 5.5 0.5 - - - +
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Residues in contact with THR 213 (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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167B ALA* 4.4 29.7 + - + +
168B GLU* 4.3 6.5 - - - +
171B GLY* 5.1 1.2 - - - -
209B VAL* 2.9 25.9 + - + +
212B ALA* 1.3 80.5 + - - +
214B ILE* 1.3 65.9 + - - +
215B PRO* 3.2 3.6 - - - -
216B ILE* 3.0 16.4 + - + +
217B THR* 3.0 27.9 + - - +
218B GLY 3.2 0.5 + - - -
219B THR* 3.5 19.3 - - - +
221B ILE* 5.9 1.6 - - + -
53D TYR* 4.7 5.5 + - - -
54D ILE* 5.3 2.3 - - - +
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 4.1 42.0 - - + +
77B ILE* 4.3 25.8 - - + -
78B ALA* 4.6 5.8 - - + +
81B PHE* 5.9 0.2 - - + -
210B HIS* 3.1 21.0 + - - +
211B LEU* 5.6 0.7 - - - +
213B THR* 1.3 75.0 - - - +
215B PRO* 1.4 70.9 - - + +
216B ILE 3.3 0.5 + - - -
217B THR 3.8 2.6 + - - -
218B GLY* 3.5 27.4 + - - +
219B THR* 3.0 24.7 + - - +
72D VAL* 5.9 3.8 - - + -
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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