Contacts of the strand formed by residues 209 - 214 (chain A) in PDB entry 1W21
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 SER 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A CYS 3.8 0.7 - - - +
201A MET* 3.2 3.8 - - - -
202A SER* 2.9 38.6 + - - -
207A ASN 4.8 2.1 + - - -
208A ALA* 1.3 77.9 - - - +
210A ALA* 1.3 64.0 + - - +
211A VAL* 4.1 6.4 + - - +
222A ILE 3.4 11.4 - - - -
223A PRO* 4.3 2.0 - - - -
230A LEU* 4.1 4.7 - - - -
2104C HIS* 5.7 1.2 - - - +
2105C ILE* 6.1 0.3 - - - +
2461C LEU* 4.0 31.0 - - - +
2462C GLY 4.4 10.6 + - - -
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Residues in contact with ALA 210 (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 ILE* 4.1 10.8 - - + -
200A CYS 3.4 5.2 - - - +
201A MET* 3.9 32.3 - - + -
209A SER* 1.3 75.2 - - - +
211A VAL* 1.3 63.1 + - - +
212A VAL* 5.2 0.9 - - + -
220A THR 4.0 0.3 - - - +
221A GLU* 3.2 6.6 - - - +
222A ILE* 2.8 52.1 + - + +
230A LEU* 3.9 3.5 - - + +
248A MET* 5.1 1.1 - - + -
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Residues in contact with VAL 211 (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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182A CYS* 5.9 0.7 - - + -
183A ILE 6.0 0.9 - - - +
199A ILE* 3.5 3.0 - - - +
200A CYS* 3.0 30.8 + - + +
209A SER* 5.1 7.6 - - - +
210A ALA* 1.3 77.9 - - - +
212A VAL* 1.3 62.3 + - - +
213A TRP* 3.1 34.5 + - + +
218A PRO* 4.2 7.0 - - + -
220A THR 3.5 6.1 - - - +
221A GLU* 4.3 4.9 - - + -
2104C HIS* 3.6 50.5 - - + +
2105C ILE* 4.0 19.1 - - + +
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A MET* 4.0 22.7 - - + -
198A SER 3.7 2.7 - - - -
199A ILE* 4.0 15.9 - - + -
210A ALA 5.1 0.7 - - - +
211A VAL* 1.3 76.7 - - - +
213A TRP* 1.3 56.9 - - - +
218A PRO* 3.7 1.2 - - - +
219A ILE* 2.7 32.7 + - - +
220A THR* 2.7 28.5 + - - +
222A ILE* 4.4 11.7 - - + -
264A PHE* 3.7 28.0 - - + -
267A GLY* 3.6 29.8 - - - +
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Residues in contact with TRP 213 (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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180A VAL 6.0 0.4 - - - -
181A GLU 3.7 18.6 - - - +
182A CYS* 3.4 27.1 - - + +
183A ILE 5.1 1.5 - - - +
196A ARG 4.4 1.1 - - - -
197A MET* 3.0 11.8 - - - +
198A SER* 2.8 40.3 + - - +
211A VAL* 3.1 35.4 - - + +
212A VAL* 1.3 77.2 - - - +
214A TYR* 1.3 60.7 + - - +
216A GLY* 3.5 32.8 - - - +
217A ARG 3.1 12.3 - - - +
218A PRO* 3.8 16.2 - - + -
2105C ILE 4.4 4.0 + - - -
2106C LEU* 3.2 52.7 - - + -
2169C MET* 4.0 17.3 - - + -
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Residues in contact with TYR 214 (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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90A PHE* 4.2 1.7 - - - -
192A ASP* 2.7 36.7 + - - -
194A MET* 3.8 10.0 - - - +
195A SER* 3.5 32.5 - - - -
196A ARG 3.4 9.9 - - - -
197A MET* 4.2 12.3 - - + -
213A TRP* 1.3 75.1 - - - +
215A GLY* 1.3 66.6 + - - +
216A GLY 3.1 0.4 - - - -
217A ARG* 2.8 22.8 + - - +
219A ILE* 3.6 21.9 - - + +
244A CYS* 6.3 0.7 - - - -
266A GLU* 3.6 55.8 + - + +
267A GLY 4.0 4.0 - - - +
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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