Contacts of the strand formed by residues 226 - 235 (chain B) in PDB entry 1H6F
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 HIS 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B CYS 3.7 9.2 - - - +
162B ARG* 4.1 19.7 - - + +
163B TYR* 4.6 0.9 - - - -
176B ALA* 3.5 26.6 - - + -
177B ASP* 3.0 41.5 + - - +
179B GLU* 3.9 13.5 - - - +
223B ASN* 3.4 26.8 + - + +
224B SER 2.9 25.4 + - - -
225B MET* 1.3 79.5 - - - +
227B LYS* 1.3 60.4 + - - +
228B TYR* 3.6 18.4 - - + +
259B ILE* 3.3 5.7 - - - -
260B ALA 3.0 24.6 + - - -
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Residues in contact with LYS 227 (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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157B ALA* 3.6 5.0 - - - +
158B ALA* 2.8 29.0 + - + -
159B ASP* 3.7 21.3 + - - +
161B CYS 4.6 2.0 + - - -
163B TYR* 3.2 44.1 + - + -
226B HIS* 1.3 73.3 - - - +
228B TYR* 1.3 69.6 + - - +
257B GLU* 3.7 34.2 + - + +
258B PHE 3.4 10.3 - - - +
259B ILE* 4.0 20.0 - - + -
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Residues in contact with TYR 228 (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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155B ILE* 3.5 15.7 - - + -
156B ILE 3.4 17.0 - - - -
157B ALA* 3.7 10.5 - - - -
158B ALA* 3.9 4.7 - - - +
179B GLU* 2.6 39.0 + - - -
182B LYS* 4.2 2.9 - - - -
222B LEU* 3.6 42.4 - - + -
223B ASN* 2.9 39.4 + - - +
226B HIS* 3.6 20.1 - - + +
227B LYS* 1.3 77.4 - - - +
229B GLN* 1.3 60.5 + - - +
230B PRO* 3.8 2.4 - - - +
257B GLU* 3.3 6.9 - - - +
258B PHE* 2.8 47.0 + + + +
260B ALA* 3.9 5.4 - - + -
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Residues in contact with GLN 229 (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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155B ILE* 3.6 1.7 - - - -
156B ILE* 2.7 42.0 + - + +
158B ALA* 4.2 13.2 - - + +
228B TYR* 1.3 74.8 - - - +
230B PRO* 1.3 85.2 - - - +
231B ARG* 3.6 5.8 + - + +
252B LEU* 4.2 18.8 - - + +
253B PHE 3.0 27.6 + - - +
254B PRO* 3.6 22.8 - - - +
256B THR* 3.4 6.4 + - - -
257B GLU* 3.9 18.1 + - - +
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Residues in contact with PRO 230 (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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132B MET* 4.1 8.7 - - + -
136B PHE* 3.9 20.7 - - + -
153B MET* 4.0 4.3 - - + -
155B ILE* 3.3 28.0 - - + -
228B TYR 3.8 4.9 - - - +
229B GLN* 1.3 108.7 - - - +
231B ARG* 1.3 58.9 + - - +
251B TYR 4.7 1.9 - - - +
252B LEU* 4.4 2.4 - - - +
253B PHE 4.7 2.3 + - - -
256B THR* 3.3 46.5 + - - +
258B PHE* 3.9 11.0 - - + -
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Residues in contact with ARG 231 (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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136B PHE* 4.8 3.8 - - - -
153B MET* 3.2 9.9 - - - +
154B ASP* 2.8 69.5 + - - +
156B ILE* 3.5 36.0 - - + +
184B MET* 4.9 3.2 - - - +
229B GLN* 3.7 9.9 - - + +
230B PRO* 1.3 82.0 - - - +
232B PHE* 1.3 60.2 + - - +
233B HIS* 3.7 22.5 + - + +
250B THR* 4.0 14.3 + - + +
251B TYR 4.0 4.5 - - - -
252B LEU* 3.7 22.7 - - + -
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Residues in contact with PHE 232 (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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105B VAL* 3.7 33.9 - - + -
136B PHE* 3.7 21.7 - + + -
138B VAL* 3.9 14.4 - - + -
140B CYS* 3.9 10.1 - - - -
151B LEU* 3.6 36.8 - - + -
152B LEU 3.4 15.9 - - - -
153B MET* 4.6 0.2 - - - +
202B VAL* 4.3 0.7 - - + -
204B PHE* 3.8 29.4 - + - -
231B ARG* 1.3 74.8 - - - +
233B HIS* 1.3 64.5 + - - +
234B ILE* 3.5 20.9 - - + -
249B ARG 3.8 0.2 - - - +
250B THR* 3.4 3.6 - - - +
251B TYR* 2.8 46.0 + + + +
253B PHE* 4.8 1.8 - - + -
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Residues in contact with HIS 233 (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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151B LEU* 3.5 6.6 - - - +
152B LEU* 2.8 50.0 + - + +
153B MET* 4.0 0.7 - - - -
154B ASP* 2.8 30.8 + - - -
184B MET* 3.6 25.0 - - + +
231B ARG* 3.7 24.9 - - + +
232B PHE* 1.3 79.2 + - - +
234B ILE* 1.3 64.7 + - - +
248B PHE* 3.6 26.5 - + + -
249B ARG 3.2 6.3 - - - +
250B THR* 2.9 39.9 + - + -
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Residues in contact with ILE 234 (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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103B PRO* 3.8 21.8 - - + -
105B VAL* 3.9 14.1 - - + -
140B CYS* 4.4 5.6 - - + -
143B LEU* 4.4 9.9 - - + -
149B TYR* 3.6 31.4 - - + -
150B ILE 4.0 1.8 - - - -
151B LEU* 3.7 11.9 - - + -
232B PHE* 3.5 19.7 - - + -
233B HIS* 1.3 72.5 - - - +
235B VAL* 1.3 66.0 + - - +
236B ARG 4.2 0.6 + - - -
247B THR 4.0 1.4 - - - +
248B PHE* 4.0 1.0 - - - -
249B ARG* 2.9 46.0 + - + +
251B TYR* 3.6 26.7 - - + -
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Residues in contact with VAL 235 (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 TYR* 3.2 7.8 - - - +
150B ILE* 2.7 43.4 + - + +
152B LEU* 3.7 20.6 - - + -
234B ILE* 1.3 78.9 - - - +
236B ARG* 1.3 60.3 + - - +
237B ALA* 3.2 25.8 + - + -
243B LEU* 3.8 14.6 - - + -
246B SER* 3.7 19.1 - - - -
247B THR 4.0 7.2 - - - +
248B PHE* 3.8 32.3 - - + -
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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