Contacts of the helix formed by residues 227 - 241 (chain B) in PDB entry 2HT6
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 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B ILE* 3.8 19.1 - - + +
219B GLU* 2.9 27.2 + - - +
220B THR* 3.7 4.0 - - + +
225B GLN 3.6 2.2 + - - -
226B HIS* 1.3 99.1 + - - +
228B VAL* 1.3 57.6 + - - +
229B LYS 3.5 2.2 - - - -
230B GLU* 3.3 25.4 + - - +
231B LEU* 3.1 26.9 + - - +
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.8 27.8 - - + +
94B ILE* 3.7 34.5 - - + -
220B THR* 4.3 3.1 - - - -
221B SER 4.1 5.2 - - - +
222B ALA* 4.2 0.7 - - - -
225B GLN* 3.9 25.3 + - + +
226B HIS 3.2 12.1 - - - +
227B ASN* 1.3 75.8 - - - +
229B LYS* 1.3 65.7 + - - +
230B GLU* 4.1 0.2 + - - -
231B LEU* 3.2 13.9 + - + +
232B PHE* 3.2 41.0 + - + -
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Residues in contact with LYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 5.8 0.4 - - - +
225B GLN 5.3 1.2 + - - -
228B VAL* 1.3 78.1 - - - +
230B GLU* 1.3 78.6 + - - +
232B PHE* 3.4 3.9 + - - +
233B GLU* 3.1 59.9 + - + +
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ILE* 4.1 14.7 - - + +
227B ASN* 3.3 34.8 + - + +
228B VAL 3.3 0.2 - - - -
229B LYS* 1.3 93.9 + - - +
231B LEU* 1.3 53.9 + - - +
233B GLU* 3.9 13.0 - - - +
234B GLY* 2.8 30.9 + - - -
237B ARG* 5.2 1.7 + - - -
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Residues in contact with LEU 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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91B LEU* 4.1 22.0 - - + -
154B LEU* 3.8 31.2 - - + -
187B ILE* 3.7 12.5 - - + +
189B VAL* 3.7 31.4 - - + -
218B ILE* 3.9 17.7 - - + +
220B THR* 4.1 20.0 - - + -
227B ASN 3.1 14.6 + - - +
228B VAL* 3.2 8.5 + - + +
230B GLU* 1.3 77.7 - - - +
232B PHE* 1.3 67.6 + - + +
234B GLY* 3.2 2.3 + - - -
235B ILE* 3.0 25.1 + - - +
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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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78B VAL* 5.5 1.6 - - + -
80B LEU* 5.4 1.1 - - + -
91B LEU* 3.8 17.5 - - + -
95B PHE* 3.4 56.1 - + + -
116B ARG* 6.3 0.2 - - - +
118B LEU* 4.3 9.4 - - + -
127B ILE* 5.8 2.0 - - + -
129B LEU* 4.0 21.1 - - + -
154B LEU* 3.5 31.2 - - + -
228B VAL* 3.2 45.3 + - + +
229B LYS* 4.1 3.4 - - - +
231B LEU* 1.3 78.8 - - + +
233B GLU* 1.3 65.8 + - - +
235B ILE* 3.3 18.2 - - + +
236B VAL* 3.2 21.5 - - - +
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 4.6 7.6 - - + -
119B MET 4.7 8.0 - - - +
120B VAL* 3.7 30.9 - - + +
229B LYS* 3.1 53.8 + - + +
230B GLU* 3.9 13.6 - - - +
232B PHE* 1.3 74.4 - - - +
234B GLY* 1.3 58.3 + - - +
236B VAL* 3.4 3.6 + - - +
237B ARG* 3.0 47.6 + - - +
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Residues in contact with GLY 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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187B ILE* 3.7 11.7 - - - -
230B GLU 2.8 22.7 + - - -
231B LEU 3.2 2.8 + - - -
233B GLU* 1.3 74.3 - - - +
235B ILE* 1.3 56.5 + - - +
237B ARG* 3.2 17.0 + - - +
238B GLN* 3.0 33.1 + - - +
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Residues in contact with ILE 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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78B VAL* 4.2 26.2 - - + -
127B ILE* 5.7 1.6 - - + -
152B ALA* 3.7 26.2 - - + -
153B TYR 3.8 19.1 - - - +
154B LEU* 3.8 14.4 - - + -
185B PRO* 4.2 9.6 - - + +
186B ILE 4.3 1.3 - - - -
187B ILE* 3.5 28.2 - - + +
231B LEU 3.0 10.4 + - - +
232B PHE* 3.3 25.8 - - + +
234B GLY* 1.3 73.0 - - - +
236B VAL* 1.3 71.8 + - + +
238B GLN* 3.3 3.9 + - + +
239B VAL* 3.1 24.9 + - - +
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Residues in contact with VAL 236 (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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76B TYR* 4.8 3.6 - - + -
118B LEU* 4.0 9.2 - - + -
120B VAL* 3.7 20.9 - - + -
125B ALA* 3.7 15.3 - - + -
127B ILE* 3.9 26.5 - - + -
232B PHE 3.2 16.4 + - - +
233B GLU 3.6 6.1 - - - +
235B ILE* 1.3 78.2 - - + +
237B ARG* 1.3 63.6 + - - +
239B VAL* 3.2 23.5 - - - +
240B ARG* 3.2 42.7 + - + +
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Residues in contact with ARG 237 (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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120B VAL* 3.9 15.6 - - + +
121B ASP* 3.1 37.0 + - - +
230B GLU 5.2 1.8 + - - -
233B GLU* 3.0 30.8 + - - +
234B GLY* 3.3 25.5 - - - +
236B VAL* 1.3 81.2 - - - +
238B GLN* 1.3 70.5 + - - +
240B ARG* 3.7 8.9 + - - +
241B LEU* 3.4 30.8 + - + +
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Residues in contact with GLN 238 (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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185B PRO* 4.0 23.1 - - + +
186B ILE 5.3 1.8 - - - +
187B ILE* 4.8 4.9 - - + -
216B LYS* 3.7 46.7 + - + +
234B GLY 3.0 21.9 + - - +
235B ILE* 3.7 9.4 - - + +
236B VAL 3.2 0.4 - - - -
237B ARG* 1.3 84.5 - - - +
239B VAL* 1.3 64.8 + - - +
241B LEU* 3.2 36.2 + - - +
242B ARG* 3.4 7.8 + - - +
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Residues in contact with VAL 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 3.5 52.6 - - + -
78B VAL* 6.1 1.3 - - + -
151B ASP* 4.3 12.3 - - + +
152B ALA* 4.5 8.7 - - + -
185B PRO* 3.8 15.5 - - + -
235B ILE 3.1 15.8 + - - +
236B VAL* 3.2 18.8 - - - +
238B GLN* 1.3 77.4 - - - +
240B ARG* 1.3 58.0 + - - +
242B ARG* 3.1 47.6 + - - +
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Residues in contact with ARG 240 (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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76B TYR* 3.6 26.9 + - + +
120B VAL* 2.7 30.5 + - - +
121B ASP* 4.3 10.5 + - - +
123B GLU* 2.9 57.0 + - - +
124B SER 3.4 11.7 + - - -
125B ALA* 3.7 12.3 - - - +
236B VAL* 3.2 28.8 + - - +
237B ARG* 3.8 8.7 - - - +
239B VAL* 1.3 73.9 - - - +
241B LEU* 1.3 59.2 + - + +
242B ARG 3.0 12.4 + - - +
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Residues in contact with LEU 241 (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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237B ARG* 3.4 21.3 + - + +
238B GLN* 3.2 32.7 + - - +
240B ARG* 1.3 76.5 - - + +
242B ARG* 1.3 57.7 + - - +
243B ARG* 3.0 21.1 + - - +
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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