Contacts of the strand formed by residues 227 - 232 (chain A) in PDB entry 4EWS
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 TYR 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ARG* 3.3 64.1 + - + -
15A ILE 3.5 12.3 - - - +
16A THR* 3.8 8.5 - - + +
76A LEU* 3.6 13.3 - - - +
222A VAL* 3.8 6.5 - - + +
223A ILE* 3.8 1.4 - - - -
224A THR* 3.0 66.1 + - + +
226A SER* 1.4 90.8 - - - +
228A LEU* 1.3 63.3 + - - +
229A GLU* 3.7 20.5 + - + -
252A PRO* 3.8 13.3 - - - +
257A ASP* 4.4 5.6 - - + -
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Residues in contact with LEU 228 (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 CYS 4.0 0.2 - - - +
14A ARG* 3.4 4.5 - - - +
15A ILE* 2.7 43.7 + - + +
20A LEU* 4.0 28.5 - - + -
76A LEU* 3.5 29.6 - - + +
82A ILE* 4.0 18.6 - - + -
129A LEU* 4.3 5.6 - - + -
222A VAL 3.3 3.1 - - - +
223A ILE* 4.0 19.7 - - + -
227A TYR* 1.3 75.9 - - - +
229A GLU* 1.3 63.9 + - - +
501A 2OB 4.4 5.4 - - + -
507A 0RP 3.3 32.5 - - + -
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Residues in contact with GLU 229 (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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7A HIS* 4.7 1.4 + - - -
12A VAL* 3.7 10.3 - - + +
13A CYS 3.3 14.8 - - - +
14A ARG* 2.8 40.6 + - + -
221A PRO* 3.3 3.0 - - - +
222A VAL* 2.5 50.0 + - + +
227A TYR* 3.7 18.9 + - + -
228A LEU* 1.3 75.8 - - - +
230A SER* 1.3 60.2 + - - +
231A HIS* 3.0 25.8 + - - +
250A PHE* 3.4 25.4 - - - -
252A PRO* 4.4 5.9 - - - +
255A LEU* 3.8 1.0 - - - +
507A 0RP 3.7 5.5 - - - -
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Residues in contact with SER 230 (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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12A VAL* 3.6 2.3 - - - +
13A CYS* 3.0 33.9 + - - +
136A VAL* 5.3 0.4 - - - -
217A LEU* 4.8 6.7 - - - -
221A PRO* 4.5 11.0 - - - -
229A GLU* 1.3 73.3 - - - +
231A HIS* 1.3 63.2 + - - +
232A HIS* 2.6 33.9 + - - -
507A 0RP 3.2 37.5 - - - -
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Residues in contact with HIS 231 (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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7A HIS* 3.6 35.6 + + + -
8A GLU 4.5 1.1 - - - +
9A ALA* 3.8 11.2 - - + -
11A ILE 3.8 4.0 - - - -
12A VAL* 3.9 20.2 - - + -
217A LEU* 3.3 9.8 - - - +
218A THR* 3.0 41.6 + - - +
219A GLY* 4.6 9.2 + - - +
220A ASP 4.5 8.3 + - - -
222A VAL* 3.6 29.4 - - + -
229A GLU* 3.0 36.9 + - - -
230A SER* 1.3 73.8 - - - +
232A HIS* 1.3 61.9 + - - +
250A PHE* 4.2 2.5 - + - -
504A PGE 5.8 0.6 + - - -
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Residues in contact with HIS 232 (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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9A ALA* 3.3 2.4 - - - +
10A GLY 2.9 24.6 + - - -
11A ILE* 2.8 27.3 + - + +
13A CYS* 4.0 2.9 - - - +
215A ILE* 2.6 36.9 + - + +
216A SER 3.4 4.0 - - - -
217A LEU* 3.6 13.2 - - + +
218A THR* 3.7 4.7 - - - -
230A SER* 2.6 37.1 + - - -
231A HIS* 1.3 71.5 - - - +
233A LYS* 1.3 62.4 + - - +
234A GLY 3.5 0.4 - - - +
507A 0RP 3.1 64.4 - - - -
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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