Contacts of the helix formed by residues 189 - 205 (chain B) in PDB entry 3F2F
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 189 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 4.3 8.1 - - + -
126B LEU* 4.0 21.5 - - + -
133B ILE* 3.8 15.7 - - + +
136B VAL* 3.8 25.1 - - + -
139B ALA 5.1 1.8 - - - +
141B MET* 3.1 29.7 + - + +
143B VAL* 4.2 11.2 - - + -
164B PHE* 4.1 16.6 - - + -
187B VAL 3.8 0.6 + - - -
188B SER* 1.3 73.2 - - - +
190B HIS* 1.3 75.2 + - + +
192B ALA* 3.3 1.7 + - - +
193B PHE* 2.9 27.2 + - - +
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Residues in contact with HIS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLU* 3.9 16.6 + - - -
133B ILE* 4.1 30.3 - - + +
136B VAL* 4.0 15.9 - - + +
139B ALA 5.3 6.2 + - - -
188B SER* 3.1 8.2 + - - +
189B VAL* 1.3 91.6 - - + +
191B GLU* 1.3 60.0 + - - +
193B PHE* 3.4 4.9 + - - +
194B GLY* 3.2 18.0 + - - -
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.4 45.3 - - - +
3B LEU* 3.7 18.5 - - + +
187B VAL* 3.9 16.8 - - + +
188B SER* 2.9 24.8 + - - +
190B HIS* 1.3 75.6 - - - +
192B ALA* 1.3 64.6 + - - +
194B GLY* 3.2 3.0 + - - -
195B LEU* 3.0 20.4 + - - +
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Residues in contact with ALA 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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3B LEU* 5.8 0.2 - - - -
98B LEU* 3.6 14.6 - - + +
101B LEU* 3.5 20.0 - - + -
143B VAL* 3.9 26.2 - - + -
145B LEU* 5.5 1.8 - - + -
187B VAL* 4.1 9.1 - - + +
188B SER 3.0 13.7 + - - +
189B VAL 3.5 4.9 - - - +
191B GLU* 1.3 77.2 - - - +
193B PHE* 1.3 56.0 + - - +
195B LEU* 3.2 11.2 + - - +
196B GLY 2.9 23.0 + - - -
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Residues in contact with PHE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.6 34.4 - - + +
105B ALA* 6.3 1.1 - - + -
128B VAL* 3.6 27.1 - - + -
129B SER 4.2 4.5 - - - -
130B PRO 4.6 4.7 - - - -
131B SER 3.8 3.6 - - - -
132B GLU* 3.5 48.2 - - - +
133B ILE* 3.7 23.1 - - + -
189B VAL 2.9 13.6 + - - +
190B HIS* 3.6 10.1 - - - +
191B GLU 3.3 0.2 - - - -
192B ALA* 1.3 75.8 - - - +
194B GLY* 1.3 59.2 + - - +
196B GLY* 3.0 3.9 + - - +
197B GLN* 2.9 58.2 + - + +
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Residues in contact with GLY 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 5.3 0.4 - - - -
190B HIS 3.2 10.8 + - - -
191B GLU* 3.2 4.9 + - - -
193B PHE* 1.3 75.6 - - - +
195B LEU* 1.3 64.5 + - - +
197B GLN* 3.1 20.2 + - - +
198B GLU* 3.0 21.3 + - - +
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Residues in contact with LEU 195 (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 LEU* 3.7 27.9 - - + +
6B TYR* 4.5 9.0 - - + -
7B ILE* 3.3 44.4 - - + +
10B LEU* 4.8 7.0 - - + -
98B LEU* 4.0 28.0 - - + -
145B LEU* 4.0 30.7 - - + -
191B GLU 3.0 7.8 + - - +
192B ALA* 3.3 9.0 - - - +
194B GLY* 1.3 76.7 - - - +
196B GLY* 1.3 63.8 + - - +
198B GLU* 3.0 6.3 + - - +
199B PHE* 2.9 20.9 + - + +
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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
----------------------------------------------------------
98B LEU* 4.5 2.0 - - - +
101B LEU* 5.4 2.7 - - - -
102B ILE* 3.6 30.4 - - - +
192B ALA 2.9 14.7 + - - -
193B PHE* 3.0 5.8 + - - -
195B LEU* 1.3 79.3 - - - +
197B GLN* 1.3 56.0 + - - +
199B PHE* 3.3 3.5 + - - +
200B ASN* 2.9 35.4 + - - -
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Residues in contact with GLN 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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130B PRO 5.5 0.6 + - - -
131B SER* 3.8 14.3 + - - +
132B GLU* 5.0 2.7 + - - +
193B PHE* 2.9 45.6 + - + +
194B GLY* 3.1 21.0 + - - +
196B GLY* 1.3 75.5 - - - +
198B GLU* 1.3 62.0 + - - +
200B ASN* 3.4 8.8 + - - +
201B ARG* 3.0 24.3 + - - +
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Residues in contact with GLU 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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7B ILE* 3.4 30.3 - - + -
194B GLY 3.0 11.7 + - - +
195B LEU* 3.0 9.6 + - - +
197B GLN* 1.3 77.1 - - - +
199B PHE* 1.3 62.5 + - - +
201B ARG* 2.7 44.8 + - - +
202B HIS* 3.1 39.5 + - + +
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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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7B ILE* 4.8 9.3 - - + +
10B LEU* 4.0 44.6 - - + -
11B LEU* 3.9 28.9 - - + -
24B LEU* 5.4 6.5 - - + -
102B ILE* 4.0 26.0 - - + -
106B LEU* 5.2 0.7 - - + -
195B LEU* 2.9 13.2 + - + +
196B GLY* 3.5 9.6 - - - +
198B GLU* 1.3 77.6 - - - +
200B ASN* 1.3 69.7 + - - +
202B HIS* 3.2 6.4 + - - +
203B LEU* 2.8 60.5 + - + +
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Residues in contact with ASN 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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101B LEU 5.1 0.8 + - - -
102B ILE* 3.0 50.0 + - - +
105B ALA* 3.4 22.1 - - + +
106B LEU* 3.5 21.2 - - + +
196B GLY 2.9 21.0 + - - +
197B GLN* 3.8 7.8 - - - +
199B PHE* 1.3 79.3 - - - +
201B ARG* 1.3 58.0 + - - +
203B LEU* 4.1 4.3 - - - -
204B LEU* 2.9 41.2 + - + +
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Residues in contact with ARG 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 GLN 3.0 17.5 + - - +
198B GLU* 2.7 35.1 + - - +
200B ASN* 1.3 78.3 - - - +
202B HIS* 1.3 83.6 + - - +
204B LEU* 3.8 4.1 - - - +
205B GLN* 3.0 62.9 + - + +
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Residues in contact with HIS 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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7B ILE* 3.9 21.2 - - + +
11B LEU* 3.4 29.6 - - + +
198B GLU* 3.1 31.5 + - + +
199B PHE 3.7 2.2 - - - +
201B ARG* 1.3 100.5 + - - +
203B LEU* 1.3 67.5 + - - +
205B GLN* 3.4 28.9 + - - +
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Residues in contact with LEU 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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11B LEU* 4.0 9.5 - - + +
21B ALA* 3.5 43.3 - - + +
24B LEU* 3.9 15.7 - - + -
25B VAL* 4.4 3.8 - - + -
106B LEU* 3.8 32.5 - - + -
199B PHE* 2.8 46.5 + - + +
200B ASN* 3.6 3.8 - - - +
202B HIS* 1.3 79.1 - - - +
204B LEU* 1.3 71.6 + - + +
205B GLN 3.2 3.5 + - - -
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Residues in contact with LEU 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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25B VAL* 3.9 23.8 - - + -
105B ALA 6.0 2.2 - - - +
106B LEU* 3.9 26.7 - - + -
200B ASN* 2.9 29.5 + - + +
201B ARG* 4.0 3.6 - - - +
203B LEU* 1.3 79.1 - - + +
205B GLN* 1.3 66.2 + - - +
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Residues in contact with GLN 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 ARG* 3.0 46.0 + - + +
202B HIS* 3.6 33.9 + - - +
203B LEU 3.2 6.2 - - - -
204B LEU* 1.3 82.2 - - - +
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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
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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