Contacts of the helix formed by residues 256 - 266 (chain A) in PDB entry 3DAE
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ASP* 3.2 4.0 + - - -
255A GLU* 1.3 76.7 - - - +
257A ILE* 1.3 67.5 + - - +
258A PRO* 3.3 11.6 - - - +
259A VAL* 2.8 43.7 + - - +
260A LEU* 2.8 11.8 + - - +
99B ARG* 3.5 19.6 + - - -
177B ASP* 3.8 7.9 + - - +
196B PHE 6.1 1.2 - - - -
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PRO* 5.2 1.6 - - + -
254A ASP 5.3 1.3 - - - +
255A GLU 3.4 4.2 + - - +
256A SER* 1.3 71.3 - - - +
258A PRO* 1.3 67.4 - - + +
260A LEU* 3.3 15.9 - - + +
261A PHE* 3.1 47.2 + - + -
176B ARG 5.2 1.1 - - - +
177B ASP* 3.3 28.0 + - - +
179B LYS* 3.4 15.3 - - - +
213B GLY 5.0 3.1 - - - +
214B SER 3.1 27.1 - - - +
215B PRO* 4.0 10.1 - - + -
218B ALA* 4.0 19.7 - - + -
222B VAL* 4.1 5.4 - - + -
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Residues in contact with PRO 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A SER* 3.1 17.5 - - - +
257A ILE* 1.3 96.5 - - + +
259A VAL* 1.3 58.7 + - + +
261A PHE* 3.2 2.4 + - + +
262A LYS* 2.8 33.3 + - - +
176B ARG* 3.3 47.1 - - + +
177B ASP* 4.2 5.2 - - + -
222B VAL* 3.9 23.2 - - + +
225B GLY* 5.6 0.3 - - - -
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASP* 3.8 16.4 - - - +
256A SER* 2.8 38.3 + - - +
258A PRO* 1.3 74.0 - - + +
260A LEU* 1.3 56.1 + - - +
262A LYS* 3.4 14.8 + - + +
263A ASN* 2.9 49.5 + - - +
99B ARG* 4.6 15.7 - - - +
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PRO* 4.3 19.5 - - + -
216A ASN* 3.8 28.9 - - - +
252A PHE* 3.2 36.1 - - + +
254A ASP* 3.9 24.8 - - + +
256A SER 2.8 11.6 + - - +
257A ILE* 3.3 20.2 - - + +
259A VAL* 1.3 75.0 - - - +
261A PHE* 1.3 63.4 + - + +
263A ASN* 3.2 6.4 + - - +
264A ILE* 3.0 42.9 + - + +
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Residues in contact with PHE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PRO* 3.6 33.2 - - + -
223A ILE* 3.8 17.2 - - + +
257A ILE* 3.1 48.2 + - + +
258A PRO 4.1 0.9 - - - +
260A LEU* 1.3 75.9 - - + +
262A LYS* 1.3 67.0 + - - +
264A ILE* 3.8 9.1 - - + +
265A SER* 3.0 25.7 + - - -
215B PRO* 3.9 10.5 - - + -
222B VAL* 3.3 28.0 - - + +
223B ILE* 3.4 45.5 - - + +
224B SER 3.6 6.3 - - - +
225B GLY* 4.3 0.4 - - - +
261B PHE* 4.0 8.7 - + - -
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A PRO 2.8 18.8 + - - +
259A VAL* 3.6 15.7 - - + +
261A PHE* 1.3 75.4 - - - +
263A ASN* 1.3 65.7 + - - +
265A SER* 2.8 22.4 + - - -
266A ASN* 2.9 30.2 + - + +
268A VAL* 6.4 0.2 - - + -
225B GLY* 4.4 15.6 - - - +
227B LEU* 5.7 14.0 - - + +
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Residues in contact with ASN 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A PHE* 3.6 32.2 + - + +
254A ASP* 4.0 9.1 + - - -
259A VAL* 2.9 37.8 + - - +
260A LEU* 3.3 8.7 - - - +
262A LYS* 1.3 80.4 - - - +
264A ILE* 1.3 56.9 + - - +
266A ASN 3.4 0.3 + - - -
267A GLY* 2.9 8.3 + - - -
268A VAL* 2.8 56.4 + - - +
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Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PRO 3.6 23.3 - - - +
216A ASN* 4.4 10.5 - - - +
218A ALA 3.7 20.6 - - - +
220A PRO* 4.2 12.6 - - - +
223A ILE* 3.8 17.0 - - + -
236A TRP* 4.0 16.0 - - + -
252A PHE* 3.9 25.8 - - + -
260A LEU* 3.0 36.8 + - + +
261A PHE* 3.8 14.6 - - + +
263A ASN* 1.3 74.9 - - - +
265A SER* 1.3 57.3 + - - +
267A GLY* 2.7 26.0 + - - -
289A VAL* 4.5 0.2 - - - +
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Residues in contact with SER 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PRO* 4.3 15.0 - - - -
223A ILE* 4.1 4.3 - - - -
261A PHE 3.0 13.5 + - - -
262A LYS* 2.8 22.7 + - - -
264A ILE* 1.3 75.5 - - - +
266A ASN* 1.3 67.2 + - - +
267A GLY 3.4 0.2 - - - -
289A VAL* 3.5 23.2 - - - +
224B SER 3.7 16.1 + - - -
225B GLY* 4.1 11.2 + - - -
226B LYS 5.3 0.4 - - - -
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Residues in contact with ASN 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LYS* 2.9 37.6 + - - +
264A ILE 3.0 0.2 - - - -
265A SER* 1.3 87.3 + - - +
267A GLY* 1.3 65.4 + - - +
268A VAL* 3.2 24.6 + - + +
289A VAL* 3.8 8.5 - - - +
225B GLY 5.6 1.7 + - - +
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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