Contacts of the helix formed by residues 251 - 263 (chain A) in PDB entry 4DBW
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 THR 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A ALA* 3.5 5.8 - - - -
250A ARG* 1.3 82.6 - - - +
252A PRO* 1.3 75.9 - - - +
253A ALA* 3.7 3.8 + - - -
254A LEU* 3.0 22.1 + - + +
255A ILE* 3.0 22.5 + - - +
279A GLN* 2.8 41.5 + - + +
401A NAP 5.6 1.3 - - - -
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Residues in contact with PRO 252 (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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236A LEU* 3.6 39.2 - - + +
241A LEU* 4.4 13.7 - - + +
242A CYS* 3.9 18.4 - - - -
245A ALA* 3.5 17.5 - - + -
251A THR* 1.3 88.0 - - - +
253A ALA* 1.3 61.6 + - - +
255A ILE* 3.2 8.2 + - + +
256A ALA* 3.0 22.9 + - - +
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Residues in contact with ALA 253 (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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219A LEU* 3.5 22.4 - - + +
236A LEU* 3.8 9.7 - - + +
251A THR* 3.2 4.2 + - - +
252A PRO* 1.3 80.5 - - - +
254A LEU* 1.3 57.7 + - - +
256A ALA 3.1 1.7 + - - -
257A LEU* 2.9 33.1 + - - +
280A ASN* 4.4 2.7 - - - +
401A NAP 3.4 45.5 - - + +
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Residues in contact with LEU 254 (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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250A ARG* 4.1 21.3 - - + -
251A THR* 3.0 28.5 + - + +
253A ALA* 1.3 78.2 - - - +
255A ILE* 1.3 57.1 + - - +
257A LEU* 3.4 6.1 + - + +
258A ARG* 2.9 31.5 + - - +
279A GLN* 3.5 35.4 - - + +
280A ASN* 3.9 11.7 - - - +
282A GLN* 3.9 15.3 - - + +
283A VAL* 3.4 38.5 - - + +
286A PHE* 3.6 14.5 - - + -
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Residues in contact with ILE 255 (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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241A LEU* 4.1 15.0 - - + +
244A LEU* 3.8 31.2 - - + +
245A ALA* 3.8 21.5 - - + +
248A HIS* 4.2 5.2 - - + -
250A ARG* 4.6 2.5 - - + -
251A THR 3.0 14.8 + - - +
252A PRO* 3.5 8.1 - - + +
254A LEU* 1.3 76.6 - - - +
256A ALA* 1.3 56.0 + - - +
258A ARG* 3.8 2.3 - - - +
259A TYR* 2.9 28.4 + - - +
286A PHE* 3.9 17.5 - - + -
288A LEU* 3.8 23.1 - - + +
296A ILE* 3.8 24.0 - - + -
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A PRO* 4.7 14.4 - - + +
218A ALA 3.6 23.6 - - - +
219A LEU* 4.2 6.1 - - + -
235A LEU* 4.6 11.7 - - + -
236A LEU* 4.6 3.4 - - + -
241A LEU* 4.8 4.5 - - + -
252A PRO 3.0 13.0 + - - +
253A ALA* 3.1 8.3 + - - +
255A ILE* 1.3 78.5 - - - +
257A LEU* 1.3 61.2 + - - +
259A TYR* 3.4 18.9 - - - +
260A GLN* 3.6 14.2 + - - +
267A VAL* 5.2 0.2 - - - +
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Residues in contact with LEU 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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19A LEU* 4.8 4.0 - - + -
218A ALA* 4.3 3.4 - - + -
219A LEU* 3.7 20.4 - - + -
253A ALA 2.9 19.6 + - - +
254A LEU* 4.0 7.0 - - + +
256A ALA* 1.3 73.8 - - - +
258A ARG* 1.3 66.4 + - - +
260A GLN* 3.2 13.2 + - - +
261A LEU* 3.3 15.8 + - - +
267A VAL* 3.7 33.5 - - + +
268A LEU 3.9 12.8 - - - +
269A ALA* 3.9 11.2 - - + -
280A ASN* 3.9 45.8 - - + +
283A VAL* 3.7 14.8 - - + -
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Residues in contact with ARG 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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254A LEU 2.9 19.4 + - - +
255A ILE 3.8 2.9 - - - +
257A LEU* 1.3 73.5 - - - +
259A TYR* 1.3 67.6 + - - +
261A LEU* 3.1 17.4 + - - +
262A GLN* 2.8 62.0 + - - +
283A VAL* 3.0 32.8 + - + +
284A PHE* 3.8 17.0 + - - +
286A PHE* 3.0 38.3 + - + +
287A GLN* 3.9 15.0 - - - +
288A LEU* 3.9 15.0 - - + +
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Residues in contact with TYR 259 (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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195A PRO* 4.2 13.5 - - + -
198A ASN* 3.6 22.6 + - + +
255A ILE 2.9 13.7 + - - +
256A ALA* 3.4 12.1 - - - +
258A ARG* 1.3 77.4 - - - +
260A GLN* 1.3 79.0 + - - +
263A ARG* 3.3 47.9 + - - -
288A LEU* 3.6 9.1 - - - +
293A MET* 3.3 40.1 - - + +
296A ILE* 3.4 45.3 + - + -
297A ASP* 2.6 32.0 + - - -
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Residues in contact with GLN 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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193A CYS* 3.4 36.3 + - - -
194A HIS* 3.6 13.9 - - - +
195A PRO* 4.8 0.4 - - - +
215A ALA* 4.2 2.2 - - + -
218A ALA* 4.7 2.8 - - + +
256A ALA 3.6 13.8 + - - +
257A LEU 3.2 6.6 + - - +
258A ARG 3.2 0.8 - - - -
259A TYR* 1.3 84.2 - - - +
261A LEU* 1.3 67.5 + - - +
263A ARG* 3.0 33.6 + - - +
265A VAL* 3.0 40.7 + - + +
267A VAL* 3.7 30.7 - - + -
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Residues in contact with LEU 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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18A VAL* 3.6 39.3 - - + +
19A LEU* 5.6 0.4 - - + -
257A LEU 3.3 10.0 + - - +
258A ARG* 3.1 23.7 + - - +
260A GLN* 1.3 76.7 - - - +
262A GLN* 1.3 62.2 + - + +
264A GLY* 3.3 13.7 + - - -
265A VAL 3.7 12.5 + - - +
267A VAL* 3.8 10.8 - - + -
283A VAL* 3.7 27.4 - - + -
284A PHE* 3.8 30.1 - - + -
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Residues in contact with GLN 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 ARG* 2.8 50.5 + - - +
260A GLN 3.2 0.2 - - - -
261A LEU* 1.3 75.3 - - - +
263A ARG* 1.3 57.6 + - - +
264A GLY 3.3 1.7 + - - -
287A GLN* 3.3 7.4 + - - +
288A LEU* 2.8 54.9 + - - +
289A THR 5.2 0.4 - - - -
293A MET* 3.8 25.2 - - + +
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Residues in contact with ARG 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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193A CYS* 3.4 9.9 - - - -
198A ASN* 2.8 45.2 + - - +
200A SER* 3.9 11.1 - - - +
203A LEU* 3.7 22.2 - - + +
207A LYS* 2.8 29.5 + - - +
259A TYR* 3.3 48.9 + - - +
260A GLN* 3.0 38.7 + - - +
262A GLN* 1.3 77.0 - - - +
264A GLY* 1.3 58.9 + - - +
265A VAL* 3.9 10.1 - - + +
293A MET* 4.1 7.2 - - + -
297A ASP* 4.5 3.8 + - - -
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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