Contacts of the strand formed by residues 215 - 221 (chain A) in PDB entry 2WOK
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 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.0 34.8 + - + +
63A LEU* 3.6 12.9 - - - -
211A SER* 2.5 28.1 + - - -
214A PRO* 1.3 104.9 - - + +
216A ARG* 1.3 57.2 + - - +
228A LEU* 4.2 17.3 - - + -
229A GLU* 3.2 25.4 - - - +
230A ARG* 4.0 15.0 - - + -
231A ASN* 3.8 2.9 - - - +
244A ALA* 3.1 29.2 + - + -
246A PRO* 2.7 43.5 + - + +
247A ASP 4.2 5.2 - - - -
249A VAL* 4.5 15.0 - - + -
554A GLN 5.7 2.7 - - - -
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Residues in contact with ARG 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.0 7.4 - - - -
110A ASP* 3.3 46.6 + - + +
209A PRO 6.0 0.9 - - - +
211A SER* 3.9 18.4 - - - -
215A TYR* 1.3 74.9 - - - +
217A VAL* 1.3 66.1 + - - +
228A LEU* 3.3 5.7 - - - -
229A GLU* 2.9 66.5 + - + +
230A ARG 3.6 11.5 + - - +
231A ASN* 4.6 1.3 - - + -
232A PRO* 3.4 29.5 - - - +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.5 14.6 - - + -
63A LEU* 4.0 24.9 - - + -
207A ARG 6.1 0.9 - - - +
209A PRO* 4.5 29.9 + - + +
211A SER* 5.4 0.2 - - - -
216A ARG* 1.3 79.7 - - - +
218A ALA* 1.3 62.1 + - - +
219A ARG 4.0 15.3 - - - +
220A HIS* 4.5 2.9 - - + +
226A LEU* 4.0 21.8 - - + -
228A LEU* 4.0 11.0 - - + -
229A GLU* 5.0 0.7 - - - +
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Residues in contact with ALA 218 (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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216A ARG 3.3 1.4 + - - -
217A VAL* 1.3 75.6 - - - +
219A ARG* 1.3 60.8 + - + +
227A HIS* 2.7 27.3 + - + +
228A LEU 4.5 0.2 - - - -
229A GLU* 3.9 36.6 - - + +
248A ARG* 5.0 5.8 - - - +
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Residues in contact with ARG 219 (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 VAL* 3.7 4.4 - - - +
218A ALA* 1.3 84.1 - - + +
220A HIS* 1.3 61.3 + - - +
221A GLU* 2.4 41.0 + - + -
225A LEU* 4.0 28.9 - - + +
226A LEU* 3.4 4.5 - - - +
227A HIS* 2.8 50.4 + - + +
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Residues in contact with HIS 220 (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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42A ASP* 2.9 39.5 + - - -
43A VAL* 4.1 14.3 - - + +
46A LEU* 3.6 23.1 - - + -
217A VAL* 4.5 4.4 - - + +
219A ARG* 1.3 76.3 - - - +
221A GLU* 1.3 65.5 + - - +
222A PRO* 3.7 27.5 - - + +
225A LEU 3.4 14.6 + - - -
226A LEU* 3.8 17.4 - - + +
253A ILE* 4.4 2.9 - - + -
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Residues in contact with GLU 221 (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 ARG* 2.4 49.6 + - + +
220A HIS* 1.3 78.6 + - - +
222A PRO* 1.3 71.4 - - + +
223A ASP 3.3 0.3 + - - -
224A THR* 2.8 42.3 + - - +
225A LEU* 2.8 29.0 + - + +
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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