Contacts of the helix formed by residues 202 - 214 (chain B) in PDB entry 4L0D
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 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B THR* 3.9 1.6 - - - -
192B PRO 5.1 0.4 - - - -
195B ALA* 3.7 13.6 - - - +
196B ARG 3.3 23.6 - - - -
197B PHE* 3.4 19.8 + - - -
199B SER 3.3 9.3 + - - -
200B PRO 3.4 0.4 - - - -
201B GLU* 1.3 79.0 - - - +
203B HIS* 1.3 71.9 + - - +
204B VAL* 3.7 2.6 + - - +
205B GLY 3.2 15.1 + - - -
206B VAL* 2.9 24.4 + - - +
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Residues in contact with HIS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO* 3.6 22.4 - - + -
146B THR 4.1 11.4 - - - -
168B VAL* 3.6 23.1 - - + +
170B PRO* 4.4 24.3 - - + +
191B THR* 3.5 25.9 + - - +
197B PHE* 5.8 3.1 - - + -
202B SER* 1.3 77.9 - - - +
204B VAL* 1.3 70.9 + - + +
206B VAL 3.5 0.2 + - - -
207B ALA* 2.9 31.0 + - - +
223B TYR* 3.2 23.3 + - - -
308B TYR* 3.7 18.8 + + - -
309B ASP* 6.0 1.1 - - - -
310B PHE* 5.2 3.6 - + - -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TRP* 3.8 11.9 - - - +
44B ILE 5.1 0.4 - - - +
46B PRO* 4.3 26.0 - - + -
145B PRO* 4.1 13.2 - - + -
197B PHE* 5.2 6.5 - - + +
202B SER* 3.3 6.0 - - - +
203B HIS* 1.3 100.6 - - + +
205B GLY* 1.3 64.2 + - - +
207B ALA* 3.2 3.8 + - - +
208B TRP* 2.9 48.8 + - + +
221B ASP* 5.5 4.3 - - - +
223B TYR* 4.3 18.6 - - + -
310B PHE* 5.1 4.5 - - + -
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Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TRP* 4.7 10.2 - - - +
197B PHE 5.2 0.9 + - - -
198B ASP 6.1 0.2 - - - -
199B SER 4.6 4.3 - - - -
200B PRO* 4.3 9.6 - - - -
202B SER* 3.2 14.9 + - - -
204B VAL* 1.3 78.2 - - - +
206B VAL* 1.3 63.2 + - - +
208B TRP* 2.9 18.5 + - - +
209B ARG* 2.9 20.8 + - - +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A HIS* 4.3 13.0 - - - +
536A ALA* 5.7 0.2 - - + -
537A ILE* 4.4 19.7 - - + -
168B VAL* 4.2 3.6 - - + -
189B VAL* 4.0 26.5 - - + -
191B THR* 3.5 18.2 - - + -
200B PRO 3.5 15.4 + - - +
201B GLU 3.8 4.9 - - - +
202B SER 2.9 18.2 + - - +
203B HIS 3.9 3.6 - - - +
205B GLY* 1.3 75.0 - - - +
207B ALA* 1.3 63.1 + - - +
209B ARG* 3.3 7.3 + - - +
210B LEU* 2.9 40.1 + - + +
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 3.9 19.0 - - + +
145B PRO* 3.8 29.6 - - + -
168B VAL* 4.2 8.3 - - + +
203B HIS 2.9 18.9 + - - +
204B VAL 3.2 6.1 - - - +
206B VAL* 1.3 78.3 - - - +
208B TRP* 1.3 57.7 + - + +
210B LEU* 3.2 6.0 + - - +
211B LYS* 2.9 22.9 + - - +
219B ILE* 3.6 13.0 - - + +
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Residues in contact with TRP 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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42B LEU* 4.5 21.1 - - + +
43B TRP* 3.2 40.4 - + + +
44B ILE* 3.9 36.6 + - + -
204B VAL* 2.9 35.7 + - + +
205B GLY 2.9 7.8 + - - +
207B ALA* 1.3 76.2 - - + +
209B ARG* 1.3 58.3 + - + +
211B LYS* 3.0 38.3 + - + +
212B ASN* 2.9 34.1 + - - +
219B ILE* 3.6 31.3 - - + +
221B ASP* 3.8 10.3 + - - -
224B ARG* 3.7 22.4 - - - -
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Residues in contact with ARG 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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537A ILE* 3.3 49.9 - - + +
538A ASP* 5.7 1.0 + - - -
541A ASN* 5.9 2.6 - - - +
200B PRO* 4.9 20.2 - - - +
205B GLY* 2.9 17.7 + - - +
206B VAL 3.7 6.5 - - - +
208B TRP* 1.3 71.7 - - + +
210B LEU* 1.3 68.0 + - - +
212B ASN* 2.8 25.5 + - - +
213B GLU* 2.9 18.8 + - + +
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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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536A ALA* 5.2 5.2 - - + -
537A ILE* 4.5 26.5 - - + +
540A LEU* 3.6 25.8 - - + -
143B ILE* 3.8 13.0 - - + -
166B ILE* 4.3 13.7 - - + -
168B VAL* 3.8 26.5 - - + -
189B VAL* 4.2 15.3 - - + -
206B VAL* 2.9 27.9 + - + +
207B ALA* 3.4 7.6 - - - +
209B ARG* 1.3 75.6 - - - +
211B LYS* 1.3 63.5 + - - +
213B GLU* 2.9 12.1 + - - +
214B ILE* 2.9 24.6 + - + +
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Residues in contact with LYS 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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42B LEU* 5.8 7.2 - - + -
143B ILE* 3.5 5.5 - - + +
207B ALA 2.9 13.1 + - - +
208B TRP* 3.0 36.3 + - + +
210B LEU* 1.3 76.1 - - - +
212B ASN* 1.3 70.0 + - - +
214B ILE 3.2 17.8 - - - +
217B SER* 3.2 37.8 + - - +
218B HIS* 4.7 3.2 - - - +
219B ILE* 3.8 31.4 - - + +
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Residues in contact with ASN 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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548A ARG* 5.8 1.0 + - - -
42B LEU* 3.6 47.6 + - - +
208B TRP* 2.9 17.0 + - - +
209B ARG* 2.8 20.9 + - - +
211B LYS* 1.3 86.1 - - - +
213B GLU* 1.3 70.0 + - - +
214B ILE 3.6 1.7 + - - +
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Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ILE* 4.7 10.8 - - + -
540A LEU* 3.7 27.6 - - + +
541A ASN* 3.0 31.8 + - - +
544A ALA* 4.3 19.5 - - + +
548A ARG* 4.7 20.5 + - - +
209B ARG* 2.9 13.8 + - + +
210B LEU 2.9 3.9 + - - +
212B ASN* 1.3 87.0 - - - +
214B ILE* 1.3 60.8 + - - +
215B PRO* 3.7 8.7 - - - +
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Residues in contact with ILE 214 (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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540A LEU* 3.6 30.1 - - + -
141B THR* 4.2 14.8 - - - +
143B ILE* 4.0 12.6 - - + -
164B ARG* 4.3 15.0 - - - +
166B ILE* 4.1 18.2 - - + -
210B LEU* 2.9 31.0 + - + +
211B LYS 3.2 6.6 - - - +
212B ASN 3.4 2.1 - - - +
213B GLU* 1.3 80.6 - - - +
215B PRO* 1.3 80.6 - - + +
216B ASN 3.7 0.7 + - - -
217B SER* 2.8 38.0 + - - +
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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