Contacts of the helix formed by residues 204 - 212 (chain B) in PDB entry 3INB
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 SER 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A LEU* 3.6 10.8 - - - +
202B SER* 3.1 4.8 + - - +
203B LEU* 1.3 79.1 - - - +
205B LEU* 1.3 57.9 + - - +
206B LEU* 3.2 7.3 + - - +
207B ASP* 3.0 30.6 + - - +
208B LEU 2.9 21.1 + - - -
228B TYR* 3.6 12.9 + - - -
256B GLU* 2.5 26.0 + - - -
270B PHE* 4.0 14.5 - - - -
272B MET 4.3 0.2 - - - +
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Residues in contact with LEU 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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203A LEU* 3.8 21.6 - - + +
263A PRO* 4.3 17.7 - - + -
269A VAL* 5.6 2.5 - - + -
204B SER* 1.3 71.3 + - - +
206B LEU* 1.3 58.1 + - - +
207B ASP 3.1 1.1 - - - -
208B LEU* 2.9 11.9 + - + +
209B TYR* 2.6 70.8 + - + -
232B TYR* 4.1 5.2 - - - +
254B VAL* 4.9 2.2 - - + -
256B GLU* 2.9 8.1 + - - +
272B MET* 3.7 19.7 - - + +
275B TYR* 3.8 39.0 - - + +
277B GLU* 3.9 4.7 - - - +
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Residues in contact with LEU 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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204B SER* 3.2 4.2 + - - +
205B LEU* 1.3 74.9 - - - +
207B ASP* 1.3 65.2 + - - +
209B TYR* 3.6 2.9 - - - +
210B LEU* 2.9 33.0 + - + +
216B VAL* 4.5 7.2 - - + -
219B ILE* 3.9 19.3 - - + -
221B THR* 4.8 7.6 - - + -
232B TYR* 3.2 55.2 + - + +
256B GLU* 3.0 20.9 + - - +
270B PHE* 6.3 2.2 - - + -
582B PHE* 3.6 35.2 - - + -
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Residues in contact with ASP 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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200B ASN 5.3 1.1 - - - +
202B SER* 2.8 34.6 + - - +
204B SER* 3.0 19.6 + - - +
205B LEU 3.1 0.4 - - - -
206B LEU* 1.3 87.2 - - - +
208B LEU* 1.3 65.1 + - - +
210B LEU* 3.6 6.4 - - - +
211B GLY* 3.0 23.2 + - - -
270B PHE* 4.8 8.9 - - - +
580B ARG* 2.8 40.8 + - - +
582B PHE* 5.4 1.8 - - - -
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Residues in contact with LEU 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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201A MET* 4.1 31.0 - - + -
202A SER 4.2 9.4 - - - +
203A LEU* 3.7 26.5 - - + -
263A PRO* 6.1 0.4 - - + -
265A LEU* 5.2 6.5 - - + -
269A VAL* 4.3 13.0 - - + -
204B SER 2.9 13.4 + - - +
205B LEU* 2.9 16.7 + - + +
207B ASP* 1.3 80.0 - - - +
209B TYR* 1.3 64.2 + - - +
210B LEU 3.1 0.2 + - - -
211B GLY 3.9 0.4 - - - -
212B ARG* 3.1 44.8 + - + +
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Residues in contact with TYR 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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263A PRO* 3.0 29.2 + - + +
265A LEU* 5.6 8.7 - - + +
205B LEU* 2.6 64.7 + - + +
206B LEU* 3.6 8.1 - - - +
208B LEU* 1.3 72.6 - - - +
210B LEU* 1.3 67.4 + - - +
212B ARG* 3.6 4.1 + - - -
213B GLY 3.6 0.7 + - - -
214B TYR* 3.3 48.6 + + + +
216B VAL* 4.7 3.6 - - + -
232B TYR* 4.6 8.3 - + + -
234B VAL* 3.0 47.3 - - + -
236B LYS* 3.2 11.1 - - + -
254B VAL* 5.7 0.4 - - + -
277B GLU* 2.6 23.1 + - - -
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Residues in contact with LEU 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 LEU* 2.9 28.2 + - + +
207B ASP* 3.6 7.2 - - - +
208B LEU 3.2 0.2 - - - -
209B TYR* 1.3 73.0 - - - +
211B GLY* 1.3 55.1 + - - +
212B ARG 2.7 0.4 + - - -
213B GLY* 2.7 31.7 + - - -
214B TYR 4.1 3.4 + - - +
216B VAL* 3.1 39.0 - - + -
219B ILE* 5.7 0.4 - - + -
582B PHE* 4.1 15.0 - - + -
595B THR* 4.3 26.5 - - + +
597B SER* 3.5 32.1 - - - +
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Residues in contact with GLY 211 (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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207B ASP 3.0 14.2 + - - -
208B LEU* 5.5 0.4 - - - -
210B LEU* 1.3 73.7 - - - +
212B ARG* 1.3 63.8 + - - +
213B GLY 3.4 1.6 - - - -
1200B NAG 5.8 7.4 - - - -
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Residues in contact with ARG 212 (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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201A MET* 3.5 36.8 - - - +
265A LEU* 4.3 15.7 - - + +
1200A NAG 2.9 43.7 + - - +
208B LEU* 3.1 32.0 + - + +
209B TYR 3.9 3.1 - - - +
210B LEU 2.7 4.6 + - - -
211B GLY* 1.3 79.1 + - - +
213B GLY* 1.3 67.2 + - - +
214B TYR* 3.6 7.1 - - + -
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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