Contacts of the strand formed by residues 208 - 214 (chain A) in PDB entry 1X3W
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 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A LYS* 5.2 1.8 - - - +
207A LEU* 1.3 74.3 - - - +
209A VAL* 1.3 61.7 + - - +
223A TYR* 3.2 5.7 - - - -
224A PHE* 3.0 47.4 + - + +
231A TRP* 3.4 9.5 - - + -
263A LYS* 5.8 3.8 - - - +
264A ASP* 4.2 14.1 - - - +
315A ARG* 3.8 29.1 + - - -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A THR* 4.2 15.7 - - + +
202A LEU* 3.7 43.1 - - + -
203A LYS* 4.0 34.3 + - + +
207A LEU* 3.5 19.1 + - + +
208A ASP* 1.3 84.9 + - - +
210A ARG* 1.3 70.4 + - - +
221A CYS* 4.1 8.1 - - + -
222A GLU 3.2 14.1 - - - +
223A TYR* 4.9 0.9 - - - -
231A TRP* 4.1 2.7 - - - -
261A PHE 4.5 0.3 - - - +
262A GLY* 3.7 14.6 - - - -
263A LYS 4.6 0.3 + - - -
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Residues in contact with ARG 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 THR* 5.0 2.0 - - - -
209A VAL* 1.3 76.2 - - - +
211A TYR* 1.3 59.8 + - - +
212A VAL 3.8 0.4 - - - +
221A CYS* 3.0 25.6 - - - +
222A GLU* 2.8 53.1 + - + +
231A TRP* 3.1 54.4 - - + +
260A ALA* 3.8 18.6 - - + -
261A PHE 3.4 6.3 - - - +
262A GLY* 4.0 16.8 - - - +
265A GLY* 4.8 3.1 + - - +
267A VAL* 3.0 30.1 - - - +
269A VAL* 3.7 8.3 - - - +
315A ARG* 5.8 1.4 - - - +
316A ASP* 5.6 3.6 + - - -
319A GLU* 2.9 30.3 + - - -
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Residues in contact with TYR 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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58A GLN* 5.5 0.7 - - - -
62A LEU* 3.6 45.3 - - + -
66A TYR* 4.0 13.9 - - + -
192A GLY 4.8 0.2 + - - -
195A CYS* 3.6 20.0 - - - -
196A ASN* 4.1 11.4 - - - -
199A THR* 3.6 25.8 - - + +
210A ARG* 1.3 72.1 - - - +
212A VAL* 1.3 63.1 + - - +
213A TRP* 4.5 8.1 - + + -
219A VAL* 3.6 34.7 - - + +
220A TRP 3.9 2.7 - - - -
221A CYS* 4.3 2.0 - - - -
260A ALA* 4.3 0.2 - - - -
261A PHE* 2.8 36.8 + + - +
1E GLC 3.2 33.8 + - - -
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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
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210A ARG 4.3 1.1 - - - +
211A TYR* 1.3 74.1 - - - +
213A TRP* 1.3 62.1 + - - +
219A VAL* 3.2 8.6 - - - +
220A TRP* 2.8 95.7 + - + +
222A GLU* 3.5 30.3 - - + +
258A CYS* 5.0 2.0 - - + -
259A ILE 3.2 10.3 - - - +
260A ALA* 4.0 9.4 - - + +
269A VAL* 4.5 6.3 - - + -
273A TYR* 4.3 7.0 - - + -
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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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51A PHE* 4.1 25.8 - + - -
54A GLY* 6.5 0.2 - - - -
55A VAL* 5.0 2.2 - - + -
58A GLN* 3.5 38.6 + - - +
211A TYR* 3.9 7.1 + + + -
212A VAL* 1.3 73.2 - - - +
214A ASN* 1.3 69.6 + - - +
215A ARG* 3.5 40.6 + - + +
219A VAL* 3.7 18.6 - - + -
257A TYR* 4.7 3.4 - - + -
258A CYS* 3.6 2.3 - - - -
259A ILE* 2.7 50.3 + - + -
261A PHE* 3.9 15.5 - - + -
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Residues in contact with ASN 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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212A VAL 4.1 1.0 + - - -
213A TRP* 1.3 82.8 + - - +
215A ARG* 1.3 65.5 + - - +
216A GLU* 2.6 42.3 + - - +
217A ASP* 3.5 6.9 + - - -
218A HIS* 2.7 28.6 + - + +
220A TRP* 3.7 18.2 - - + -
253A LYS* 4.0 6.0 - - - +
255A MSE 2.5 54.1 - - - +
257A TYR 3.4 10.0 - - - +
258A CYS* 3.9 6.1 - - - -
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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