Contacts of the helix formed by residues 202 - 211 (chain B) in PDB entry 3Q8Q
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 ASN 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 3.5 7.6 - - - +
30B ILE* 3.8 12.5 - - - +
200B ALA* 3.4 1.2 + - - +
201B SER* 1.3 82.9 + - - +
203B LYS* 1.3 58.4 + - - +
204B LEU* 3.2 8.0 + - - +
205B LEU* 2.9 33.5 + - - +
206B ALA* 3.0 29.3 + - - +
287B GLY 3.1 24.7 + - - -
288B GLU* 4.3 1.0 - - - +
289B ASP* 3.2 35.9 + - - +
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Residues in contact with LYS 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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28B ARG* 4.8 1.4 - - - +
30B ILE* 4.2 4.9 - - + +
121B GLU* 2.8 38.4 + - - -
129B PHE* 3.3 49.6 - - + -
202B ASN* 1.3 72.1 - - - +
204B LEU* 1.3 66.7 + - - +
207B LYS* 3.0 21.1 + - - +
289B ASP* 3.6 9.0 + - - +
291B SER* 3.6 34.3 + - - +
292B PRO 3.5 16.9 + - - +
293B VAL* 3.9 17.3 - - + -
294B ILE* 5.5 0.4 - - - +
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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
----------------------------------------------------------
202B ASN* 3.4 6.7 - - - +
203B LYS* 1.3 76.5 - - - +
205B LEU* 1.3 59.1 + - + +
207B LYS* 3.4 3.9 + - - +
208B LEU* 2.9 49.6 + - + +
230B ILE* 5.5 0.4 - - + -
239B ILE* 4.4 7.2 - - + -
240B PRO* 3.5 31.9 - - + +
284B LEU* 3.6 43.1 - - + +
287B GLY* 3.7 25.8 - - - +
289B ASP* 3.1 21.1 + - + +
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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
----------------------------------------------------------
200B ALA* 3.6 16.2 - - + -
201B SER* 4.1 13.7 - - - +
202B ASN* 2.9 28.3 + - - +
204B LEU* 1.3 76.2 - - + +
206B ALA* 1.3 61.8 + - - +
208B LEU* 3.8 5.0 - - + +
209B VAL* 2.8 33.8 + - - +
221B LEU* 4.0 15.3 - - + -
226B CYS* 3.8 29.6 - - + +
229B LEU* 4.0 18.0 - - + +
230B ILE* 4.3 9.2 - - + -
287B GLY* 3.5 29.8 - - - +
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Residues in contact with ALA 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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30B ILE* 3.9 23.1 - - + +
32B HIS* 3.6 14.3 - - + +
129B PHE* 4.9 0.2 - - + -
198B GLY* 3.6 17.2 - - - +
200B ALA* 3.6 9.8 - - - +
202B ASN 3.0 18.4 + - - +
203B LYS 3.8 3.8 - - - +
205B LEU* 1.3 76.0 - - - +
207B LYS* 1.3 58.3 + - - +
209B VAL* 3.5 6.9 - - - +
210B SER* 3.0 31.4 + - - -
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Residues in contact with LYS 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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32B HIS* 3.6 24.9 - - + +
34B ASP* 5.3 0.8 + - - -
123B LEU* 4.0 7.4 - - + -
127B GLU* 2.8 35.8 + - - +
129B PHE* 4.0 14.4 - - + -
203B LYS 3.0 17.7 + - - +
204B LEU* 3.8 3.6 - - - +
206B ALA* 1.3 76.0 - - - +
208B LEU* 1.3 65.5 + - + +
210B SER* 3.1 14.4 + - - -
211B GLY 4.2 2.1 + - - -
240B PRO* 4.0 31.0 - - + -
872P C 4.0 6.7 - - - -
873P C 2.8 29.9 + - - -
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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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204B LEU* 2.9 45.6 + - + +
205B LEU* 3.9 9.2 - - + +
207B LYS* 1.3 78.1 - - + +
209B VAL* 1.3 62.2 + - - +
211B GLY* 4.0 5.5 + - - -
212B VAL* 3.8 11.4 + - - +
229B LEU* 3.8 26.0 - - + +
230B ILE* 4.9 8.1 - - + -
233B LEU* 4.1 31.9 - - + -
238B GLU 4.0 10.5 - - - +
239B ILE* 5.6 0.9 - - + -
240B PRO* 3.9 22.0 - - + -
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Residues in contact with VAL 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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158B TYR* 3.9 30.5 - - + -
198B GLY* 3.5 15.9 - - - -
199B VAL 3.8 13.7 - - - +
205B LEU 2.8 19.7 + - - +
206B ALA* 3.5 8.5 - - - +
208B LEU* 1.3 76.3 - - - +
210B SER* 1.3 64.7 + - - +
211B GLY 3.2 2.9 - - - -
212B VAL* 3.1 18.5 + - + +
219B THR* 3.5 30.8 - - - +
221B LEU* 4.0 13.7 - - + +
229B LEU* 3.9 8.5 - - + -
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Residues in contact with SER 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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32B HIS* 2.8 33.6 + - - -
34B ASP* 4.3 7.8 + - - +
196B CYS* 3.4 24.0 - - - +
197B ALA* 3.6 8.6 - - - +
198B GLY* 3.2 30.5 - - - +
206B ALA 3.0 10.7 + - - -
207B LYS 3.1 8.0 + - - -
208B LEU 3.4 0.2 - - - -
209B VAL* 1.3 76.8 - - - +
211B GLY* 1.3 61.0 + - - +
212B VAL 3.6 0.7 + - - -
213B PHE 4.0 6.1 + - - +
217B GLN 4.7 0.3 - - - +
219B THR* 4.8 1.8 - - - +
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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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34B ASP* 6.0 2.0 - - - -
207B LYS 4.2 1.8 + - - -
208B LEU 4.0 5.8 + - - -
209B VAL 3.2 0.6 - - - -
210B SER* 1.3 83.4 + - - +
212B VAL* 1.3 63.3 + - - +
213B PHE 3.3 1.8 - - - -
214B LYS* 3.2 34.0 - - - +
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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