Contacts of the helix formed by residues 196 - 210 (chain B) in PDB entry 4I5L
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 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B GLU* 4.0 31.0 - - + +
152B PHE* 3.5 42.5 - - + -
158B GLU* 3.0 36.8 + - + +
195B SER* 1.3 70.8 - - - +
197B HIS* 1.3 63.6 + - + +
199B PHE* 3.4 0.7 + - - +
200B VAL* 2.8 41.3 + - + +
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Residues in contact with HIS 197 (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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195B SER* 3.3 8.0 + - - +
196B VAL* 1.3 85.4 - - + +
198B LYS* 1.3 62.0 + - - +
200B VAL* 3.9 5.2 - - - +
201B ALA* 3.0 34.7 + - + +
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Residues in contact with LYS 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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186B ALA* 3.4 26.5 + - - +
187B GLY* 4.8 9.8 + - - -
194B VAL* 4.0 9.0 - - + -
195B SER* 3.3 19.9 + - - +
197B HIS* 1.3 81.5 + - - +
199B PHE* 1.3 66.2 + - - +
201B ALA* 3.4 6.9 + - + +
202B MET* 3.3 22.7 + - - +
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Residues in contact with PHE 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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148B ILE* 3.9 20.4 - - + -
152B PHE* 3.6 21.8 - + + -
165B MET* 4.4 4.9 - - - -
168B VAL* 3.4 29.2 - - + -
172B CYS* 3.6 24.0 - - - -
182B LEU* 3.7 31.9 - - + -
186B ALA* 3.7 23.8 - - + -
194B VAL* 4.1 9.9 - - + +
195B SER 3.0 17.1 + - - +
196B VAL 3.9 1.6 - - - +
198B LYS* 1.3 77.4 - - - +
200B VAL* 1.3 62.6 + - - +
202B MET* 3.4 18.2 + - + +
203B TRP* 3.1 26.5 + - + +
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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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145B ILE* 3.8 37.7 - - + +
148B ILE* 3.7 27.6 - - + -
149B GLU* 4.2 10.1 - - + +
196B VAL* 2.8 33.1 + - + +
197B HIS* 3.9 5.4 - - - +
199B PHE* 1.3 71.7 - - - +
201B ALA* 1.3 65.6 + - - +
203B TRP* 3.2 3.7 + - - +
204B ARG* 2.9 45.4 + - - +
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Residues in contact with ALA 201 (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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197B HIS* 3.0 27.4 + - + +
198B LYS* 3.6 8.3 - - + +
199B PHE 3.4 0.2 - - - -
200B VAL* 1.3 77.7 - - - +
202B MET* 1.3 61.0 + - + +
204B ARG* 3.8 20.1 + - - +
205B LYS* 3.4 19.8 + - - +
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Residues in contact with MET 202 (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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182B LEU* 3.7 24.9 - - + +
185B GLY* 4.3 12.8 - - - +
186B ALA* 4.0 20.0 - - + -
198B LYS 3.3 8.9 + - - +
199B PHE* 3.6 25.8 - - + +
200B VAL 3.2 0.4 - - - -
201B ALA* 1.3 78.3 - - + +
203B TRP* 1.3 82.3 + - + +
205B LYS* 3.4 10.9 + - + +
206B ILE* 3.2 32.3 + - - +
220B LEU* 3.7 29.2 - - + -
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Residues in contact with TRP 203 (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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144B VAL* 3.9 5.0 - - + +
145B ILE* 5.1 0.4 - - + -
148B ILE* 3.6 26.9 - - + -
172B CYS* 3.7 21.4 + - + +
174B CYS* 3.7 31.2 - - - -
178B TRP* 4.4 6.1 - + - -
182B LEU* 3.5 27.1 - - + -
199B PHE* 3.1 26.8 + - + +
200B VAL 4.2 1.6 - - - +
202B MET* 1.3 81.4 - - + +
204B ARG* 1.3 60.7 + - - +
206B ILE* 3.3 34.1 + - + +
207B LEU* 2.9 72.6 + - + +
216B LYS* 4.3 15.9 - - + -
220B LEU* 4.2 11.0 - - + -
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Residues in contact with ARG 204 (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 VAL* 4.2 12.6 - - + -
142B ASP* 5.9 1.4 + - - -
145B ILE* 4.1 24.1 - - + +
200B VAL* 2.9 35.5 + - - +
201B ALA* 3.9 25.0 + - - +
203B TRP* 1.3 76.1 - - - +
205B LYS* 1.3 55.8 + - - +
207B LEU* 3.2 7.0 + - - +
208B GLN* 2.9 63.7 + - - +
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Residues in contact with LYS 205 (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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201B ALA 3.4 11.5 + - - +
202B MET* 3.4 13.7 + - + +
203B TRP 3.2 0.4 - - - -
204B ARG* 1.3 79.0 - - - +
206B ILE* 1.3 64.4 + - + +
208B GLN* 3.3 7.3 + - - -
209B ASN* 2.7 44.2 + - - +
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Residues in contact with ILE 206 (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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202B MET* 3.3 24.7 - - - +
203B TRP* 3.5 42.4 - - + +
205B LYS* 1.3 81.2 - - + +
207B LEU* 1.3 58.5 + - - +
209B ASN 3.2 0.3 + - - -
210B CYS* 2.8 40.8 + - + +
216B LYS* 3.8 32.5 - - + -
219B HIS* 3.8 37.5 - - + +
220B LEU* 4.6 4.9 - - + +
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Residues in contact with LEU 207 (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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139B VAL* 4.5 28.4 - - + +
141B VAL* 4.2 28.9 - - + +
144B VAL* 3.9 24.9 - - + -
145B ILE* 4.7 2.0 - - + -
172B CYS 5.8 0.7 - - - +
203B TRP* 2.9 64.3 + - + +
204B ARG 3.6 5.2 - - - +
206B ILE* 1.3 77.4 - - + +
208B GLN* 1.3 60.4 + - - +
209B ASN 3.6 0.2 + - - -
210B CYS 3.9 11.0 - - - +
211B HIS* 4.6 5.2 + - - -
216B LYS* 4.1 21.8 - - - +
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Residues in contact with GLN 208 (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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132B ARG* 6.2 0.2 - - - +
141B VAL* 4.9 17.0 - - + +
204B ARG* 2.9 47.4 + - + +
205B LYS* 3.8 9.0 - - - +
206B ILE 3.2 0.4 - - - -
207B LEU* 1.3 79.1 - - - +
209B ASN* 1.3 68.9 + - - +
211B HIS* 3.7 14.2 + - - -
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Residues in contact with ASN 209 (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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132B ARG* 4.5 31.8 + - + +
205B LYS* 2.7 40.0 + - - +
206B ILE 3.2 1.8 + - - +
208B GLN* 1.3 90.8 + - - +
210B CYS* 1.3 68.0 + - - +
211B HIS* 4.0 15.5 + - - -
215B ALA* 5.6 0.3 - - - +
219B HIS* 5.2 10.1 + - + +
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Residues in contact with CYS 210 (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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206B ILE* 2.8 26.1 + - - +
207B LEU 3.9 6.4 - - - +
209B ASN* 1.3 84.4 - - - +
211B HIS* 1.3 64.1 + - - +
212B ASP 3.6 1.3 - - - -
215B ALA* 3.7 8.7 - - + -
216B LYS* 3.7 41.9 - - + +
219B HIS* 3.4 50.5 - - - -
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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