Contacts of the helix formed by residues 250 - 262 (chain A) in PDB entry 3EWS
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 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A MET 3.5 5.9 + - - +
248A ILE 3.2 4.4 - - - +
249A ALA* 1.3 80.9 - - - +
251A GLN* 1.3 66.1 + - - +
252A GLY* 3.2 19.1 - - - +
253A HIS* 2.9 47.0 + - + +
254A GLN* 3.3 8.5 + - - +
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Residues in contact with GLN 251 (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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248A ILE 4.3 1.2 + - - -
249A ALA 3.9 2.4 + - - -
250A THR* 1.3 72.2 - - - +
252A GLY* 1.3 62.7 + - - +
254A GLN* 3.2 38.5 + - - +
255A ASP* 3.2 41.4 + - - +
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Residues in contact with GLY 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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250A THR* 3.0 12.6 - - - +
251A GLN* 1.3 79.3 - - - +
253A HIS* 1.3 62.4 + - - +
254A GLN 3.2 0.2 + - - -
255A ASP* 3.4 5.1 + - - +
256A GLN* 3.0 39.6 + - - +
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Residues in contact with HIS 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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170A PRO* 3.3 29.6 + - + +
217A THR* 4.9 4.6 - - - -
218A PRO* 3.5 25.6 - - + +
219A GLY 5.0 1.3 + - - -
246A VAL 5.4 1.0 + - - -
247A MET* 3.2 41.5 + - + +
249A ALA* 6.1 0.2 - - - +
250A THR* 2.9 29.6 + - + +
252A GLY* 1.3 75.4 - - - +
254A GLN* 1.3 59.7 + - - +
256A GLN* 3.7 14.0 - - - +
257A SER* 3.0 29.5 + - - -
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Residues in contact with GLN 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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247A MET 4.5 0.4 - - - +
248A ILE* 3.2 45.6 + - - +
250A THR 3.3 8.0 + - - +
251A GLN* 3.2 32.4 + - - +
252A GLY 3.2 0.4 - - - -
253A HIS* 1.3 74.2 - - - +
255A ASP* 1.3 69.7 + - - +
257A SER* 2.9 13.9 + - - -
258A ILE* 3.0 19.1 + - + +
280A SER* 5.9 2.6 + - - -
284A PHE* 3.9 34.7 - - + +
287A LYS* 5.8 2.8 - - - -
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Residues in contact with ASP 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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251A GLN* 3.2 34.5 + - - +
252A GLY* 4.0 5.1 + - - +
254A GLN* 1.3 78.5 - - - +
256A GLN* 1.3 60.4 + - + +
258A ILE* 3.6 7.8 + - - +
259A ARG* 3.0 44.6 + - - +
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Residues in contact with GLN 256 (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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199A ARG* 5.9 0.4 - - - +
218A PRO* 3.5 22.0 - - + +
219A GLY* 3.4 31.2 + - - -
222A LEU* 4.5 15.7 - - + +
252A GLY* 3.0 30.6 + - - +
253A HIS* 3.7 8.0 - - - -
255A ASP* 1.3 78.3 - - + +
257A SER* 1.3 61.2 - - - +
259A ARG* 3.3 11.3 + - - +
260A ILE* 3.0 31.5 + - - +
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Residues in contact with SER 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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168A LEU* 3.6 25.1 - - - +
218A PRO* 3.8 9.0 - - - +
239A PHE* 4.5 3.4 - - - -
241A LEU* 3.9 23.1 - - - +
247A MET* 3.9 9.7 - - - +
253A HIS 3.0 21.3 + - - -
254A GLN 2.9 4.8 + - - -
256A GLN* 1.3 73.8 - - - +
258A ILE* 1.3 60.2 + - - +
260A ILE* 3.1 4.2 + - - +
261A GLN* 2.9 30.1 + - - +
284A PHE* 4.1 7.6 - - - -
288A VAL* 5.2 1.6 - - - -
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Residues in contact with ILE 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 GLN* 3.0 16.4 + - + +
255A ASP* 3.7 10.5 - - - +
257A SER* 1.3 75.3 - - - +
259A ARG* 1.3 64.8 + - + +
261A GLN* 3.1 8.2 + - - +
262A ARG* 3.1 57.1 + - + +
284A PHE* 4.1 9.9 - - + -
287A LYS* 3.6 44.2 - - + +
288A VAL* 3.4 28.7 - - + -
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Residues in contact with ARG 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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222A LEU* 3.8 37.3 - - + +
255A ASP* 3.0 30.2 + - - +
256A GLN* 3.8 12.7 - - - +
257A SER 3.2 0.4 - - - -
258A ILE* 1.3 78.1 - - + +
260A ILE* 1.3 61.8 + - - +
262A ARG* 4.0 23.0 + - - +
263A MET* 3.5 18.9 + - - +
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Residues in contact with ILE 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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166A LEU* 4.2 17.9 - - + -
168A LEU* 3.9 16.4 - - + -
218A PRO* 3.4 28.0 - - + +
221A VAL* 3.7 13.9 - - + -
222A LEU* 3.6 31.0 - - + +
225A CYS* 4.9 8.1 - - + -
233A PRO* 5.8 0.2 - - - +
239A PHE* 4.2 19.1 - - + -
256A GLN 3.0 18.7 + - - +
257A SER* 3.5 5.8 - - - +
259A ARG* 1.3 75.4 - - - +
261A GLN* 1.3 65.8 + - - +
262A ARG 3.1 2.0 - - - -
263A MET* 2.9 22.1 + - + +
264A LEU* 3.8 8.6 + - + +
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Residues in contact with GLN 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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239A PHE* 4.2 12.8 - - + -
257A SER 2.9 16.6 + - - +
258A ILE* 3.1 7.1 + - - +
260A ILE* 1.3 76.3 - - - +
262A ARG* 1.3 73.7 + - - +
263A MET 3.5 0.5 + - - -
264A LEU* 3.5 25.3 + - - +
270A MET* 3.5 28.5 - - - +
287A LYS 4.3 8.8 - - - +
288A VAL* 3.1 44.2 + - + +
290A PRO* 3.9 15.2 - - - +
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Residues in contact with ARG 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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234A LYS* 5.2 1.7 + - - -
258A ILE* 3.1 39.4 + - + +
259A ARG* 4.1 19.2 - - - +
260A ILE 3.1 1.2 - - - -
261A GLN* 1.3 87.5 - - - +
263A MET* 1.3 60.9 + - + +
264A LEU 3.2 5.4 - - - +
287A LYS* 5.7 4.6 - - - +
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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