Contacts of the helix formed by residues 204 - 216 (chain B) in PDB entry 6H7L
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 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B TRP 2.6 30.1 + - - -
182B TRP 3.0 10.6 + - - -
183B ARG 3.2 19.8 + - - +
184B ASP* 3.9 17.3 - - - +
203B THR* 1.3 85.0 + - - +
205B ARG* 1.3 65.1 + - - +
206B ALA* 3.3 9.2 + - - +
207B TYR* 2.7 34.8 + - - +
208B ALA 3.5 5.7 + - - -
314B VAL* 3.5 4.9 - - - +
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Residues in contact with ARG 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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204B ASN* 1.3 73.2 - - - +
206B ALA* 1.3 66.2 + - - +
208B ALA* 3.1 4.5 + - - +
209B ILE* 3.0 41.5 + - + +
314B VAL* 3.5 39.2 + - + +
315B PHE* 3.3 34.7 + - - +
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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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204B ASN* 3.3 8.8 + - - +
205B ARG* 1.3 79.1 - - - +
207B TYR* 1.3 58.4 + - - +
209B ILE* 3.5 5.9 + - - +
210B ALA* 2.9 33.1 + - - +
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Residues in contact with TYR 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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122B VAL* 3.7 12.4 - - + +
172B VAL* 2.8 30.6 + - + -
176B PRO* 3.5 27.1 - - + -
177B ILE* 3.4 24.0 - - + +
181B TRP* 4.9 1.6 - - + +
182B TRP* 3.9 22.4 - - + -
201B PHE* 4.2 13.2 - + - -
203B THR* 3.5 26.0 - - + -
204B ASN* 2.7 23.7 + - - +
206B ALA* 1.3 73.4 - - - +
208B ALA* 1.3 57.5 + - - +
210B ALA* 4.6 4.0 - - + -
211B SER* 2.8 55.8 + - - -
405B Y00 4.9 0.2 - - - -
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Residues in contact with ALA 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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201B PHE* 6.0 0.2 - - + -
203B THR* 3.3 24.0 - - + +
204B ASN 3.5 2.2 + - - -
205B ARG 3.1 2.2 + - - -
207B TYR* 1.3 80.7 - - - +
209B ILE* 1.3 62.1 + - - +
211B SER* 3.6 5.3 + - - -
212B SER* 2.7 31.6 + - - -
310B ASN* 4.1 20.6 - - - +
311B ILE* 3.4 4.5 - - + +
314B VAL* 3.4 25.1 - - + -
405B Y00 5.2 0.2 - - - -
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Residues in contact with ILE 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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205B ARG* 3.0 44.4 + - + +
206B ALA* 3.9 5.4 - - - +
208B ALA* 1.3 76.3 - - + +
210B ALA* 1.3 60.1 + - - +
212B SER* 3.2 3.5 + - - -
213B ILE* 2.9 51.5 + - + +
311B ILE* 3.6 24.0 - - + -
314B VAL* 4.8 4.5 - - + -
315B PHE* 4.3 15.0 - - + -
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Residues in contact with ALA 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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172B VAL* 5.3 0.2 - - - -
206B ALA 2.9 22.9 + - - +
207B TYR* 4.0 4.3 - - + +
209B ILE* 1.3 75.3 - - - +
211B SER* 1.3 56.7 + - - +
213B ILE* 3.4 6.1 + - - +
214B ILE* 2.9 45.8 + - + +
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Residues in contact with SER 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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172B VAL* 3.9 23.1 - - - -
207B TYR* 2.8 46.8 + - - -
208B ALA* 3.6 4.2 + - - -
210B ALA* 1.3 73.5 - - - +
212B SER* 1.3 57.2 + - - +
215B SER* 2.7 35.7 + - - -
405B Y00 2.8 32.3 + - - -
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Residues in contact with SER 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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208B ALA 2.7 21.3 + - - -
209B ILE 3.2 3.9 + - - -
211B SER* 1.3 75.8 + - - +
213B ILE* 1.3 61.5 + - - +
216B PHE* 2.9 27.2 + - - +
217B TYR* 3.1 19.9 + - - -
307B PHE* 3.5 21.9 - - - -
310B ASN* 3.1 24.4 + - - +
311B ILE* 3.7 16.8 - - - +
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Residues in contact with ILE 213 (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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209B ILE* 2.9 40.5 + - + +
210B ALA* 3.8 6.5 - - - +
212B SER* 1.3 76.4 - - - +
214B ILE* 1.3 64.7 + - + +
217B TYR* 3.3 23.9 + - + -
218B ILE* 2.9 54.7 + - + +
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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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126B THR* 4.7 3.1 - - + -
130B GLU* 2.9 32.9 - - - +
168B ILE* 3.8 11.0 - - + -
172B VAL* 3.7 35.2 - - + -
210B ALA* 2.9 30.4 + - + +
211B SER 4.3 2.2 - - - +
213B ILE* 1.3 81.6 - - + +
215B SER* 1.3 62.4 + - - +
218B ILE* 4.9 9.6 - - + -
219B PRO* 3.6 12.7 - - - +
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Residues in contact with SER 215 (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 VAL* 5.1 0.7 - - - -
126B THR* 2.6 39.7 + - - +
129B ILE* 3.2 29.7 - - - +
130B GLU 4.5 1.4 + - - -
172B VAL* 4.5 3.6 - - - +
211B SER* 2.7 24.7 + - - -
214B ILE* 1.3 78.8 - - - +
216B PHE* 1.3 55.4 + - - +
219B PRO* 3.6 4.1 - - - +
307B PHE* 4.1 14.4 - - - -
405B Y00 2.9 16.0 + - - -
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Residues in contact with PHE 216 (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 ILE* 4.1 4.7 - - + -
212B SER 2.9 12.5 + - - +
214B ILE 3.5 0.8 - - - -
215B SER* 1.3 79.6 - - - +
217B TYR* 1.3 92.4 + + - +
218B ILE 3.6 0.9 - - - -
219B PRO* 3.5 5.0 - - - +
220B LEU* 2.8 46.1 + - + +
299B PHE* 3.6 27.8 - + - -
300B THR* 5.2 2.7 - - + -
303B TRP* 3.5 29.6 - - + -
304B LEU* 3.6 39.3 - - + -
307B PHE* 3.6 32.8 - + + -
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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