Contacts of the helix formed by residues 186 - 204 (chain B) in PDB entry 4F4I
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 PRO 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ARG* 5.1 1.3 - - - +
184B ASP 3.9 2.0 - - - +
185B GLN* 1.3 90.8 - - + +
187B LEU* 1.3 66.4 + - - +
188B GLU* 3.2 7.2 - - + +
189B ASN* 3.0 32.9 + - - +
190B VAL 3.2 6.8 + - - -
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Residues in contact with LEU 187 (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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13B SER 4.8 0.9 - - - +
14B GLY* 4.4 23.8 - - - +
17B THR* 4.4 26.9 - - + +
18B VAL* 4.5 5.6 - - + -
141B ARG* 3.5 41.5 - - - +
186B PRO* 1.3 73.5 - - - +
188B GLU* 1.3 62.2 + - - +
190B VAL* 3.8 17.7 - - + +
191B VAL* 3.0 33.5 + - + +
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 5.0 2.6 + - - +
186B PRO* 4.5 5.9 - - + +
187B LEU* 1.3 78.6 - - - +
189B ASN* 1.3 66.8 + - - +
191B VAL* 3.6 8.5 - - - +
192B GLU* 3.5 18.7 + - - +
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Residues in contact with ASN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLN* 3.4 29.2 + - + +
186B PRO* 3.0 32.1 + - - +
188B GLU* 1.3 82.7 - - - +
190B VAL* 1.3 66.0 + - - +
191B VAL 3.2 1.6 - - - -
192B GLU* 3.9 6.6 - - - +
193B ASP* 3.1 31.6 + - - +
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER 4.8 1.1 - - - +
18B VAL* 3.7 22.4 - - + -
131B LEU* 4.2 12.1 - - + -
181B VAL* 3.8 19.6 - - + +
182B ASN 3.4 20.9 - - - +
183B ALA* 3.8 15.3 - - + -
185B GLN 3.4 25.1 - - - +
186B PRO 3.2 4.2 + - - +
187B LEU* 3.2 17.0 + - + +
189B ASN* 1.3 76.8 - - - +
191B VAL* 1.3 58.4 + - - +
194B THR* 2.7 37.8 + - - +
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 5.5 2.2 - - + -
18B VAL* 4.4 17.7 - - + +
21B GLU* 4.1 37.0 - - + +
22B VAL* 3.8 21.2 - - + +
25B ARG* 3.8 24.5 - - - +
187B LEU* 3.0 25.7 + - + +
188B GLU* 3.6 8.7 - - - +
190B VAL* 1.3 73.7 - - - +
192B GLU* 1.3 55.7 + - - +
194B THR* 3.1 4.5 + - - -
195B TYR* 2.7 36.0 + - + +
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Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 2.8 38.7 + - - +
188B GLU 3.5 10.7 + - - +
189B ASN* 4.0 9.6 - - - +
190B VAL 3.5 0.2 - - - -
191B VAL* 1.3 78.4 - - - +
193B ASP* 1.3 70.6 + - - +
195B TYR* 3.2 4.5 + - - +
196B GLN* 2.9 60.1 + - + +
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Residues in contact with ASP 193 (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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181B VAL* 3.8 21.0 - - + +
182B ASN* 4.9 1.9 + - - +
185B GLN* 2.9 26.7 + - - +
189B ASN* 3.1 18.0 + - - +
192B GLU* 1.3 82.8 - - - +
194B THR* 1.3 52.0 + - - +
196B GLN* 3.9 7.0 - - - +
197B THR* 2.4 37.6 + - - -
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Residues in contact with THR 194 (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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7B PHE* 3.5 31.9 - - + -
18B VAL* 3.8 10.6 - - + +
22B VAL* 3.6 16.4 - - + -
129B ILE* 4.0 10.5 - - + -
131B LEU* 4.1 5.4 - - - +
181B VAL* 3.8 19.0 - - - +
190B VAL 2.7 24.1 + - - -
191B VAL 3.4 4.5 - - - -
193B ASP* 1.3 75.0 - - - +
195B TYR* 1.3 65.1 + - - +
197B THR* 3.4 4.6 - - - -
198B ILE* 3.0 27.7 + - + +
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Residues in contact with TYR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 4.2 17.0 - - + +
25B ARG* 3.4 63.1 + - + +
26B LEU* 3.8 27.3 - - + +
28B LYS* 5.7 2.3 - - - +
29B ASP* 4.1 15.9 + - - -
30B TYR* 5.4 1.6 - - - -
191B VAL* 2.7 20.4 + - + +
192B GLU* 3.6 7.4 - - - +
194B THR* 1.3 75.1 - - - +
196B GLN* 1.3 69.4 + - - +
198B ILE* 3.5 2.8 + - - +
199B ILE* 3.0 58.3 + - + +
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Residues in contact with GLN 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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55A ASN* 6.3 1.8 - - - +
25B ARG* 5.3 0.2 - - - +
192B GLU* 2.9 55.2 + - + +
193B ASP* 3.9 6.7 - - - +
195B TYR* 1.3 84.0 - - - +
197B THR* 1.3 61.3 + - - +
199B ILE* 3.6 18.8 - - - +
200B LYS* 2.8 33.5 + - - +
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Residues in contact with THR 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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55A ASN* 5.6 6.9 + - - +
127B LEU* 4.6 2.8 - - + +
129B ILE* 3.6 26.9 - - + -
179B LYS* 3.6 37.5 - - + +
181B VAL* 4.0 10.3 - - + +
193B ASP 2.4 24.9 + - - -
194B THR* 3.4 7.4 - - - -
196B GLN* 1.3 77.6 - - - +
198B ILE* 1.3 61.7 + - - +
200B LYS* 3.7 7.9 - - - +
201B TYR* 3.1 21.7 + - - +
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Residues in contact with ILE 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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5B ILE* 3.8 29.6 - - + -
7B PHE* 3.6 23.6 - - + -
22B VAL* 3.4 32.5 - - + -
26B LEU* 3.7 27.4 - - + -
89B LEU* 5.1 1.6 - - + -
127B LEU* 4.4 6.3 - - + -
129B ILE* 4.4 9.2 - - + -
194B THR* 3.0 19.7 + - + +
195B TYR 3.5 4.2 + - - +
196B GLN 3.3 0.2 - - - -
197B THR* 1.3 75.0 - - - +
199B ILE* 1.3 63.4 + - - +
201B TYR* 3.0 6.1 + - - +
202B LEU* 3.0 35.9 + - + +
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Residues in contact with ILE 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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26B LEU* 3.5 26.9 - - + -
30B TYR* 4.0 16.6 - - + +
195B TYR* 3.0 51.2 + - + +
196B GLN* 3.6 24.5 - - - +
198B ILE* 1.3 73.0 - - - +
200B LYS* 1.3 67.1 + - - +
202B LEU* 3.7 6.6 - - - +
203B GLU* 2.8 48.1 + - - +
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Residues in contact with LYS 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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55A ASN* 4.2 28.5 - - - +
56A ASP* 5.2 10.9 - - - +
179B LYS* 5.0 21.1 - - + +
196B GLN 2.8 21.4 + - - +
197B THR* 3.7 7.2 - - - +
199B ILE* 1.3 78.4 - - - +
201B TYR* 1.3 63.8 + - - +
203B GLU* 3.6 8.9 + - - -
204B LYS* 3.4 48.9 + - - +
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Residues in contact with TYR 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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3B ALA* 4.3 16.4 - - + -
5B ILE* 4.7 3.8 - - + -
126B ASP* 3.1 46.7 + - + +
127B LEU* 3.7 32.8 - - + -
176B GLN 5.9 2.0 - - - -
179B LYS* 6.3 4.3 - - - -
197B THR 3.1 13.1 + - - +
198B ILE 3.0 9.7 + - - +
200B LYS* 1.3 79.2 - - - +
202B LEU* 1.3 74.7 + - + +
204B LYS 3.7 15.6 + - - -
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Residues in contact with LEU 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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3B ALA* 4.1 17.3 - - + -
5B ILE* 4.7 4.0 - - + -
26B LEU* 4.6 2.2 - - + -
30B TYR* 3.9 46.9 - - + +
87B VAL* 4.0 28.3 - - + -
198B ILE* 3.0 33.5 + - + +
199B ILE* 3.2 6.7 + - - +
201B TYR* 1.3 84.8 - - + +
203B GLU* 1.3 65.0 + - - +
204B LYS* 3.4 2.9 + - - +
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Residues in contact with GLU 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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30B TYR* 4.2 12.5 + - - +
199B ILE* 2.8 58.4 + - - +
200B LYS* 3.7 7.2 + - - +
202B LEU* 1.3 77.3 - - - +
204B LYS* 1.3 71.2 + - + +
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Residues in contact with LYS 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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200B LYS* 3.4 53.9 + - - +
201B TYR 3.7 14.1 - - - -
202B LEU 3.3 2.7 - - - +
203B GLU* 1.3 92.2 + - + +
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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