Contacts of the strand formed by residues 206 - 214 (chain Q) in PDB entry 3HOU
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 GLY 206 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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942M PHE* 3.8 17.0 - - - -
946M VAL* 3.5 11.8 - - - +
1016M THR* 4.6 0.2 - - - -
1017M LEU* 3.2 21.1 - - - +
201Q LYS* 3.2 8.5 - - - -
202Q SER 2.8 37.3 + - - -
205Q SER* 1.3 68.1 - - - +
207Q ARG* 1.3 64.4 + - - +
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Residues in contact with ARG 207 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942M PHE* 3.4 32.5 - - + -
1012M ARG* 5.2 6.3 + - - +
1013M ASP* 3.1 45.4 + - - +
1014M ALA 4.5 0.2 + - - -
1016M THR* 4.1 20.6 + - - +
199Q ILE* 4.5 19.3 - - + +
200Q ARG 3.4 7.9 - - - +
201Q LYS* 3.9 17.5 - - + +
202Q SER* 4.3 0.9 - - - +
205Q SER* 2.7 24.1 + - - +
206Q GLY* 1.3 77.9 - - - +
208Q TYR* 1.3 60.7 + - - +
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Residues in contact with TYR 208 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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865M GLN* 3.6 5.9 - - + -
866M PHE* 2.6 49.1 + - + +
867M ILE* 4.1 15.9 - - + -
870M GLU* 3.2 53.8 - - + +
1013M ASP* 4.8 4.7 - - + -
1373M ASP* 6.0 0.2 - - - -
198Q ILE 3.9 0.9 - - - +
199Q ILE* 3.6 4.9 - - - +
200Q ARG* 2.9 59.5 + - - +
202Q SER* 4.3 4.5 - - - -
205Q SER* 4.4 0.9 - - - +
207Q ARG* 1.3 76.8 - - - +
209Q ALA* 1.3 76.9 + - - +
210Q SER* 3.7 20.1 + - - -
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Residues in contact with ALA 209 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866M PHE* 4.2 5.7 - - - +
1010M ALA* 6.2 1.1 - - + -
1013M ASP* 4.3 19.6 + - - +
197Q LYS* 3.8 29.6 - - - +
198Q ILE 3.6 4.0 - - - -
199Q ILE* 4.4 5.2 - - + +
208Q TYR* 1.3 93.3 + - - +
210Q SER* 1.3 61.1 + - - +
211Q TYR* 4.0 14.9 - - + +
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Residues in contact with SER 210 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866M PHE* 3.9 12.9 - - - -
1342M GLU* 5.2 4.0 + - - -
176Q PRO* 5.0 4.7 - - - +
197Q LYS* 3.5 2.8 - - - +
198Q ILE* 2.8 45.0 + - - +
200Q ARG* 4.7 9.6 + - - -
208Q TYR* 3.7 21.4 + - - -
209Q ALA* 1.3 74.1 - - - +
211Q TYR* 1.3 81.7 + - - +
212Q ARG* 5.5 2.1 + - - +
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Residues in contact with TYR 211 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866M PHE* 3.6 27.8 - + + -
1006M ILE* 4.1 13.0 - - - +
156Q LEU* 4.4 9.9 - - + -
164Q LEU* 3.2 49.9 - - + +
168Q TYR* 4.8 6.3 - + - -
175Q LEU* 3.9 10.3 - - + -
176Q PRO* 3.2 30.3 - - - +
195Q VAL* 4.3 1.6 - - + -
196Q VAL 3.6 12.6 - - - +
197Q LYS* 3.8 45.2 + - + +
198Q ILE* 4.6 0.4 - - - +
209Q ALA* 4.0 17.7 - - + +
210Q SER* 1.3 82.3 + - - +
212Q ARG* 1.3 63.3 + - - +
213Q ILE 4.3 0.2 - - - -
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Residues in contact with ARG 212 (chain Q).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1341M ILE* 3.9 18.9 - - - +
1342M GLU* 2.5 36.8 + - - +
1345M ARG* 5.4 4.4 - - - +
1373M ASP* 5.8 1.2 + - - -
1376M THR* 3.7 35.6 + - - -
1377M THR* 3.9 10.3 + - - +
176Q PRO* 2.7 13.9 + - - +
177Q ARG 2.7 35.8 + - - -
178Q ILE* 3.6 15.5 - - + +
195Q VAL* 3.5 3.9 - - - -
196Q VAL* 2.9 54.4 + - + +
198Q ILE* 3.3 15.5 - - + +
210Q SER* 5.5 2.3 + - - +
211Q TYR* 1.3 74.7 - - - +
213Q ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 213 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161Q LYS* 4.4 0.2 - - - +
172Q GLU* 3.5 51.6 - - + +
175Q LEU* 3.9 25.6 - - + +
176Q PRO 2.8 7.9 + - - -
177Q ARG* 3.2 27.3 - - + +
178Q ILE* 2.6 34.9 + - - +
193Q GLY* 3.9 9.0 - - - +
194Q GLU 3.6 12.3 - - - +
195Q VAL* 3.7 14.8 - - + +
211Q TYR 4.3 0.2 - - - -
212Q ARG* 1.3 74.1 - - - +
214Q CYS* 1.3 64.4 + - - +
215Q MET* 5.3 2.2 - - - -
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Residues in contact with CYS 214 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178Q ILE* 3.5 11.2 - - + -
179Q GLN 4.8 0.9 - - - -
180Q ARG* 4.1 16.6 - - - -
190Q LEU* 3.9 32.3 - - + -
191Q LYS 4.0 4.3 - - - +
192Q ARG* 3.5 21.5 + - - -
193Q GLY* 3.3 24.7 + - - +
194Q GLU 3.0 18.8 + - - +
213Q ILE* 1.3 78.0 - - - +
215Q MET* 1.3 77.6 + - - +
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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