Contacts of the strand formed by residues 207 - 216 (chain A) in PDB entry 1U5U
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 VAL 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A GLY 4.9 3.4 - - - +
206A LYS* 1.3 72.5 - - - +
208A ARG* 1.3 66.3 + - - +
209A TYR* 3.7 22.0 - - + +
277A GLU* 3.7 4.0 - - - +
278A ALA* 2.8 46.1 + - + +
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Residues in contact with ARG 208 (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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86A PRO* 3.5 25.4 - - - +
199A PRO* 3.8 1.7 - - - +
200A PHE* 2.9 38.9 + - + +
202A ALA* 3.4 17.4 - - - +
204A ASP* 2.6 43.6 + - - -
206A LYS* 3.4 29.2 + - - +
207A VAL* 1.3 80.8 - - - +
209A TYR* 1.3 74.6 + - - +
275A ILE* 3.5 26.9 - - + +
276A HIS 3.3 8.3 - - - +
277A GLU* 3.9 25.0 + - + +
278A ALA 4.4 0.4 - - - +
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Residues in contact with TYR 209 (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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197A THR* 3.7 16.8 - - + -
198A MET 3.0 14.1 - - - +
199A PRO* 4.2 2.2 - - + -
200A PHE* 3.9 3.5 - - - +
207A VAL* 3.7 19.9 - - + +
208A ARG* 1.3 78.8 - - - +
210A CYS* 1.3 64.9 + - - +
275A ILE* 3.5 9.7 - - - +
276A HIS* 2.9 44.8 + + - +
278A ALA* 4.0 22.7 - - + +
286A ILE* 4.0 19.9 - - + +
287A PHE* 3.8 22.8 - + - -
293A TRP* 3.8 9.6 - + + -
334A LEU* 3.9 32.1 - - + -
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Residues in contact with CYS 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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196A VAL 3.5 2.1 - - - +
197A THR* 3.9 0.5 - - - -
198A MET* 2.7 44.5 + - - +
199A PRO 4.1 9.9 - - - -
200A PHE* 4.0 13.5 - - + -
209A TYR* 1.3 76.9 - - - +
211A ARG* 1.3 69.3 + - - +
212A TYR* 4.0 23.5 - - - -
273A ILE* 3.5 31.6 - - + -
274A GLN 3.3 8.5 - - - +
275A ILE* 3.8 4.9 - - + -
293A TRP* 3.7 2.7 - - - -
331A LEU* 4.9 0.2 - - - -
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Residues in contact with ARG 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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140A GLU 5.9 0.6 + - - -
194A SER* 3.9 6.7 - - - +
195A GLN* 3.3 20.7 + - - +
196A VAL 3.9 9.6 - - - +
197A THR* 3.0 24.6 + - - -
210A CYS* 1.3 81.7 - - - +
212A TYR* 1.3 65.2 + - - +
273A ILE* 3.5 3.0 - - - -
274A GLN* 3.0 56.8 + - + +
286A ILE 3.6 5.9 + - - -
288A HIS 3.0 30.3 + - - -
289A ALA* 3.8 8.9 + - - +
291A ILE 3.1 21.2 + - - -
292A LEU* 4.1 3.6 - - - +
293A TRP* 3.3 39.6 - - + +
300A TRP* 3.3 5.9 - - + -
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Residues in contact with TYR 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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91A PHE* 3.6 18.8 - + - -
132A LEU* 4.6 4.1 - - + +
134A ILE* 3.9 42.4 - - + -
136A MET* 4.0 1.6 - - - -
193A TYR* 3.5 3.6 - - - +
194A SER* 2.8 44.9 + - - +
195A GLN 4.4 0.9 + - - -
198A MET* 4.4 17.9 - - - -
210A CYS* 4.0 16.3 - - - -
211A ARG* 1.3 76.8 - - - +
213A ARG* 1.3 65.8 + - - +
271A LEU* 4.6 3.4 - - + -
272A GLN 3.5 14.8 - - - +
273A ILE* 3.7 21.5 - - + -
300A TRP* 3.7 6.1 - - - -
303A LEU* 3.7 22.0 - - + -
327A GLN* 5.3 0.9 + - - -
331A LEU* 3.6 21.3 - - - +
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Residues in contact with ARG 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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136A MET* 3.5 6.5 - - - -
191A TYR* 3.9 24.1 - - - -
192A TYR 2.9 18.6 - - - +
193A TYR* 3.0 37.5 + - + -
212A TYR* 1.3 78.6 - - - +
214A ALA* 1.3 60.1 + - - +
215A LEU* 4.2 13.5 - - + +
223A GLU* 4.2 2.2 + - - -
271A LEU* 3.6 4.3 - - - +
272A GLN* 2.8 58.9 + - + +
300A TRP* 3.5 51.5 - - + +
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Residues in contact with ALA 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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119A PHE* 3.7 40.4 - - + -
136A MET* 3.8 12.5 - - + -
190A LEU 3.6 2.6 - - - +
191A TYR* 3.5 5.0 - - - +
192A TYR* 2.9 33.2 + - + +
213A ARG* 1.3 77.1 - - - +
215A LEU* 1.3 61.2 + - - +
269A TYR* 5.0 3.8 - - + -
270A ARG 3.4 9.2 - - - +
271A LEU* 4.6 4.3 - - + -
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Residues in contact with LEU 215 (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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190A LEU 3.9 3.1 - - - -
191A TYR* 3.7 39.5 - - + +
213A ARG* 4.2 9.9 - - - +
214A ALA* 1.3 78.1 - - - +
216A PRO* 1.3 76.0 - - + +
269A TYR* 3.4 9.8 - - - +
270A ARG* 2.7 65.8 + - + +
272A GLN* 3.5 37.5 - - + +
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Residues in contact with PRO 216 (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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188A ALA 3.3 23.3 - - - +
189A HIS* 4.0 16.2 - - + +
190A LEU 3.6 16.1 - - - +
191A TYR* 4.4 7.0 - - + -
215A LEU* 1.3 95.4 - - + +
217A GLY* 1.3 60.8 + - - +
219A VAL* 3.4 38.3 - - + +
221A ILE* 4.4 15.5 - - + +
268A ASN 4.2 2.7 - - - +
269A TYR* 4.6 1.3 - - + -
270A ARG* 3.8 14.3 + - - -
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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