Contacts of the helix formed by residues 201 - 206 (chain B) in PDB entry 3M9M
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 LYS 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ILE 4.1 5.4 - - - +
176B ARG 3.2 26.9 - - - +
177B GLU* 2.5 27.3 + - - +
178B LEU 3.5 16.6 - - - +
179B ASP* 4.1 8.3 - - - +
180B ILE* 4.1 6.3 - - - -
199B ILE* 3.6 8.9 - - - +
200B ASN* 1.3 98.0 - - + +
202B LEU* 1.3 67.7 + - - +
203B VAL* 3.3 5.6 - - + +
204B ASP* 3.1 29.7 + - - +
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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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149B VAL* 6.4 0.4 - - + -
150B PHE* 4.0 28.7 - - + -
153B ILE* 6.0 0.4 - - + -
174B LEU 5.1 1.3 - - - +
175B ILE* 3.4 30.0 + - + +
178B LEU* 4.2 9.9 + - + +
180B ILE* 4.4 7.0 - - + +
183B VAL* 4.3 22.4 - - + -
201B LYS* 1.3 72.8 - - - +
203B VAL* 1.3 53.9 + - - +
204B ASP 2.7 11.6 + - - -
205B THR* 2.7 28.2 + - - -
225B LEU* 3.5 45.8 - - + +
228B LEU* 3.7 20.2 - - + +
229B ALA* 3.5 5.4 - - + +
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 2.8 36.7 + - + +
176B ARG* 4.4 20.4 - - + +
201B LYS* 4.6 6.5 - - + -
202B LEU* 1.3 71.3 - - - +
204B ASP* 1.3 72.3 - - - +
205B THR 3.2 2.4 + - - -
206B LEU* 3.6 27.6 + - + +
207B SER* 4.5 3.6 + - - -
229B ALA* 4.3 5.4 - - - +
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Residues in contact with ASP 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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198B GLY 3.6 20.3 - - - +
199B ILE* 3.8 21.2 - - + +
200B ASN* 4.1 2.6 + - - +
201B LYS* 3.1 34.1 + - - +
202B LEU 2.7 6.1 + - - -
203B VAL* 1.3 82.3 - - - +
205B THR* 1.3 57.6 + - - -
206B LEU 3.4 0.4 - - - -
207B SER* 3.3 25.6 + - - -
208B ILE* 3.7 8.8 - - - +
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 4.4 5.6 - - + -
199B ILE* 4.0 21.8 - - + -
202B LEU* 2.7 20.9 + - - +
204B ASP* 1.3 77.5 - - - +
206B LEU* 1.3 61.7 + - - +
207B SER 3.3 2.2 - - - -
208B ILE* 3.5 21.5 - - - +
210B PHE* 6.0 0.5 - - - -
213B LEU* 4.1 22.4 - - + +
225B LEU* 3.9 27.7 + - + -
226B ILE* 3.9 19.2 - - - +
229B ALA* 3.3 16.1 - - - +
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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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203B VAL* 3.6 24.4 + - + +
204B ASP 3.4 0.8 - - - -
205B THR* 1.3 77.8 - - - +
207B SER* 1.3 60.3 + - - +
208B ILE 4.3 2.3 - - - +
226B ILE* 3.6 15.7 - - + -
229B ALA* 3.5 37.5 - - + +
230B ARG* 3.4 36.1 - - + +
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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