Contacts of the helix formed by residues 196 - 202 (chain B) in PDB entry 4FE1
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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126B ILE 4.1 5.4 - - - +
127B GLY* 4.3 4.9 - - - +
192B HIS* 2.6 47.8 + - + +
194B ILE 3.5 0.6 - - - -
195B HIS* 1.3 84.4 - - + +
197B ALA* 1.3 58.0 + - - +
198B ILE 3.3 1.3 - - - -
199B PRO* 3.2 3.1 - - - +
200B GLU* 2.7 51.5 + - + +
206B VAL* 3.8 30.3 - - + +
207B GLY* 5.7 1.1 - - - -
211B PHE* 6.1 2.2 - - + -
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Residues in contact with ALA 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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125B THR 3.6 18.8 - - - +
126B ILE 3.8 18.5 + - - +
127B GLY* 4.4 1.6 - - - +
129B ARG* 4.8 1.6 + - - -
192B HIS* 3.5 2.5 + - + +
193B LEU* 3.5 38.2 + - + +
196B VAL* 1.3 78.1 - - - +
198B ILE* 1.3 57.9 + - - +
200B GLU* 3.5 1.7 + - - +
201B SER* 2.9 30.3 + - - -
269B LEU* 3.5 9.2 - - + +
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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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193B LEU* 2.8 24.5 + - + +
194B ILE* 3.8 17.0 - - + +
197B ALA* 1.3 71.6 - - - +
199B PRO* 1.4 73.4 - - + +
201B SER* 2.4 28.5 + - - +
202B ARG* 3.0 49.5 + - - +
216B PRO 5.8 0.9 - - - +
252B ALA 4.1 2.0 - - - +
253B ILE* 3.9 19.5 - - + +
269B LEU* 3.7 23.8 - - + -
270B THR* 3.7 27.4 - - + +
273B ALA* 4.3 2.9 - - + -
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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
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194B ILE 3.1 25.8 - - - +
195B HIS* 3.3 16.8 - - - +
196B VAL 3.2 11.0 - - - +
198B ILE* 1.4 89.0 - - + +
200B GLU* 1.3 57.0 + - - +
202B ARG* 3.0 16.8 + - + +
204B GLN* 2.8 43.7 + - - +
206B VAL* 3.4 25.8 - - + -
216B PRO* 5.0 11.4 - - + +
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Residues in contact with GLU 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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127B GLY* 3.8 21.2 - - - +
129B ARG* 3.3 41.3 + - - +
133B ASP* 5.4 0.7 - - - +
196B VAL* 2.7 39.4 + - + +
197B ALA 4.0 2.0 - - - +
199B PRO* 1.3 66.8 - - - +
201B SER* 1.3 60.3 + - - +
202B ARG 3.0 5.9 + - - -
203B GLY* 3.3 10.6 + - - -
204B GLN 3.1 10.6 + - - +
205B HIS* 2.7 49.4 + - - +
206B VAL 3.1 12.3 + - - +
244B GLY* 3.6 6.8 - - - +
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Residues in contact with SER 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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129B ARG* 3.8 6.5 - - - +
197B ALA 2.9 15.1 + - - -
198B ILE* 2.4 31.6 + - - +
200B GLU* 1.3 76.9 - - - +
202B ARG* 1.3 61.3 + - - +
203B GLY 3.4 1.6 - - - -
241B HIS* 3.3 16.3 + - - -
243B PHE* 3.5 17.9 - - - -
244B GLY 2.6 27.1 + - - +
269B LEU* 3.4 18.9 - - - +
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Residues in contact with ARG 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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198B ILE* 3.3 28.8 - - - +
199B PRO* 3.0 11.7 + - + +
201B SER* 1.3 85.0 + - - +
203B GLY* 1.3 61.3 + - - +
204B GLN* 3.2 7.1 + - + +
216B PRO 5.0 3.2 + - - -
236B PRO 3.3 12.1 + - - -
237B ASP* 3.0 37.1 + - - +
241B HIS* 4.7 1.1 - - + +
245B THR 3.3 20.5 - - - +
246B ALA* 3.6 10.0 + - - +
249B ALA* 3.7 15.2 - - + +
250B GLY 3.2 18.9 + - - -
251B THR* 3.1 19.6 + - - +
252B ALA* 2.8 34.2 + - - +
253B ILE* 4.9 1.6 - - - +
270B THR* 3.9 4.8 - - - +
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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
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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