Contacts of the helix formed by residues 300 - 305 (chain A) in PDB entry 2WEA
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 ASP 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASP 4.3 3.3 - - - +
15A GLU 4.2 7.4 - - - +
16A GLU* 4.3 2.4 - - - -
17A TYR* 3.5 28.8 - - + -
157A LEU* 3.2 21.5 - - + +
214A THR* 2.8 31.3 - - - +
215A GLY 5.2 0.3 - - - -
216A THR 2.8 18.0 + - - +
217A THR* 3.3 18.6 + - - +
299A GLY* 1.3 72.3 - - - -
301A ILE* 1.3 63.7 + - - +
303A LEU* 3.9 5.8 - - - +
304A LYS* 2.9 33.8 + - - +
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Residues in contact with ILE 301 (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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217A THR 3.1 15.4 + - - +
218A LEU* 3.7 5.6 - - + -
219A LEU* 4.0 13.9 - - + +
267A VAL* 3.8 22.4 - - + +
271A LEU* 3.5 30.4 - - - +
272A ILE* 4.6 5.4 - - + -
274A TYR* 4.2 20.9 - - + -
286A GLY* 3.6 41.7 - - - +
299A GLY 3.3 0.4 - - - -
300A ASP* 1.3 76.5 - - - +
302A PHE* 1.3 62.5 + - - +
304A LYS* 3.8 31.7 + - - +
305A SER 4.3 1.4 + - - -
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Residues in contact with PHE 302 (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 PHE* 5.1 0.9 - + - -
219A LEU* 4.1 22.8 - - + +
256A PHE* 5.7 1.8 - + - -
258A VAL* 4.1 5.8 - - + -
260A ILE* 4.5 5.4 - - + -
265A ALA* 3.8 32.3 - - + -
267A VAL* 3.6 28.7 - - + -
298A PHE* 3.6 44.6 - + + -
299A GLY 3.0 8.3 + - - +
301A ILE* 1.3 79.5 - - - +
303A LEU* 1.3 77.7 + - + +
305A SER* 2.7 27.0 + - - -
306A GLN* 3.9 18.5 - - + +
319A PHE* 4.1 22.9 - + - -
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Residues in contact with LEU 303 (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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155A VAL* 5.3 5.2 - - + -
157A LEU* 4.0 17.8 + - + +
212A ALA* 4.8 13.7 - - + -
213A ASP 4.0 1.3 - - - +
214A THR* 3.7 43.1 - - + +
298A PHE 3.7 17.7 - - - +
299A GLY 3.0 20.1 + - - +
300A ASP* 3.2 6.3 + - - +
302A PHE* 1.3 84.6 - - + +
304A LYS* 1.3 58.3 + - - +
305A SER 3.0 6.3 + - - -
306A GLN* 2.9 29.4 + - - +
308A VAL* 3.9 27.7 - - + +
310A PHE* 5.2 2.7 - - + -
319A PHE* 5.7 0.2 - - + -
322A GLN* 3.5 2.6 + - - -
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Residues in contact with LYS 304 (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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13A ASN 4.5 2.8 + - - -
14A ASP* 2.8 35.1 + - - +
17A TYR* 3.2 25.4 - - - +
157A LEU* 3.2 20.3 - - + +
158A LYS* 3.7 11.7 - - - +
159A HIS* 3.8 15.3 + - + +
217A THR 5.5 0.4 + - - -
271A LEU* 4.1 22.8 + - + +
274A TYR* 5.2 2.2 + - - +
300A ASP* 2.9 30.2 + - - +
301A ILE* 3.8 30.8 - - - +
302A PHE 3.2 0.2 - - - -
303A LEU* 1.3 75.1 - - - +
305A SER* 1.3 58.4 + - - +
306A GLN 3.4 0.2 - - - -
322A GLN* 3.5 15.6 + - - +
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Residues in contact with SER 305 (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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266A THR 3.5 20.5 + - - +
267A VAL* 3.9 10.2 - - - +
268A PRO* 4.2 5.4 - - - -
271A LEU* 3.9 17.5 - - - +
302A PHE* 2.7 19.2 + - - -
303A LEU 3.0 1.4 - - - -
304A LYS* 1.3 80.6 - - - +
306A GLN* 1.3 78.0 + - - +
321A PRO* 3.7 3.8 - - - +
322A GLN* 3.0 19.5 + - - +
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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