Contacts of the strand formed by residues 267 - 277 (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 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A ALA* 3.6 22.4 - - + -
258A TYR* 3.6 20.0 - - + +
261A ARG* 4.0 26.0 - - + +
262A LEU* 3.8 23.1 - - + +
265A GLY 4.2 1.6 - - - +
266A PRO* 1.3 72.4 - - - +
268A ASN* 1.3 63.4 + - - +
269A TYR* 3.3 37.0 - - + +
306A VAL 3.5 0.5 - - - +
308A ILE* 2.8 32.5 + - + +
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Residues in contact with ASN 268 (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* 5.2 1.0 - - - +
216A PRO* 4.2 1.2 - - - +
217A GLY* 3.0 25.2 + - - +
218A ASP* 2.7 37.6 + - - +
266A PRO* 3.9 18.3 + - - +
267A VAL* 1.3 78.2 - - - +
269A TYR* 1.3 67.1 + - - +
305A LYS* 3.7 25.7 + - - +
306A VAL 3.1 5.2 - - - +
307A SER* 2.6 32.7 + - - -
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Residues in contact with TYR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.8 11.4 - - + -
103A HIS* 2.7 34.2 - + - -
119A PHE* 3.7 21.1 - + + -
187A PHE 4.5 1.3 - - - -
188A ALA* 4.0 22.1 - - - -
190A LEU 5.9 0.2 - - - -
192A TYR* 5.0 4.5 - + - -
214A ALA* 5.0 3.1 - - + -
215A LEU 3.4 16.6 - - - +
217A GLY* 3.9 1.8 - - - +
258A TYR* 2.6 34.3 + - - -
267A VAL* 3.3 28.9 - - + +
268A ASN* 1.3 78.9 - - - +
270A ARG* 1.3 66.2 + - - +
271A LEU 3.9 0.2 - - - -
305A LYS* 3.7 8.1 - - - +
306A VAL* 2.7 53.3 + - + -
308A ILE* 3.8 2.5 - - + -
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Residues in contact with ARG 270 (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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214A ALA* 3.4 2.9 - - - -
215A LEU* 2.7 64.5 + - + +
216A PRO 3.8 18.3 + - - +
217A GLY* 4.2 9.6 - - - -
219A VAL 5.8 1.6 + - - -
220A ASP* 5.4 5.7 + - - -
269A TYR* 1.3 73.7 - - - +
271A LEU* 1.3 61.4 + - - +
272A GLN* 3.5 13.2 - - - +
302A ASP* 3.1 40.6 + - - +
304A ALA 3.9 3.4 - - - -
305A LYS* 5.1 1.6 - - + +
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Residues in contact with LEU 271 (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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77A ILE* 5.1 0.4 - - + -
119A PHE* 5.1 0.2 - - + -
121A ILE* 4.2 11.4 - - + -
123A PHE* 4.2 14.4 - - + -
134A ILE* 4.0 22.9 - - + -
136A MET* 3.8 22.9 - - + -
212A TYR* 4.6 3.6 - - + -
213A ARG 3.6 16.2 - - - +
214A ALA* 4.5 4.0 - - + +
269A TYR 3.9 1.6 + - - -
270A ARG* 1.3 71.7 - - - +
272A GLN* 1.3 58.2 + - - +
302A ASP* 3.7 1.6 - - - +
303A LEU* 2.7 57.0 + - + -
304A ALA* 2.9 27.7 + - + +
306A VAL* 4.0 14.8 - - + +
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Residues in contact with GLN 272 (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 TYR* 3.5 10.0 - - - +
213A ARG* 2.8 69.7 + - + +
215A LEU* 3.5 25.8 - - + +
270A ARG* 3.5 17.1 - - - +
271A LEU* 1.3 79.5 - - - +
273A ILE* 1.3 64.8 + - - +
300A TRP* 3.5 24.4 + - + +
301A PHE 3.2 12.8 - - - +
302A ASP* 3.0 30.5 + - - +
303A LEU* 3.8 2.5 - - - +
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Residues in contact with ILE 273 (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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85A PHE* 4.2 24.5 - - + -
91A PHE* 4.6 4.0 - - + -
200A PHE* 3.7 18.2 - - + -
210A CYS* 3.5 22.7 - - + -
211A ARG 3.5 14.1 - - - +
212A TYR* 3.7 25.1 - - + -
272A GLN* 1.3 77.7 - - - +
274A GLN* 1.3 67.7 + - - +
275A ILE* 3.7 11.2 - - + -
300A TRP* 3.5 5.2 - - - -
301A PHE* 2.9 42.0 + - + +
303A LEU* 4.1 15.9 - - + -
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Residues in contact with GLN 274 (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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193A TYR* 5.9 0.4 - - - -
210A CYS* 3.3 6.8 - - - +
211A ARG* 3.0 58.6 + - + +
273A ILE* 1.3 75.2 - - - +
275A ILE* 1.3 64.1 + - - +
292A LEU* 5.9 4.2 - - - +
293A TRP* 3.6 29.9 - - + +
295A LYS* 5.8 0.9 - - - -
298A HIS* 3.0 34.2 - - - +
299A PRO 3.8 7.9 - - - +
300A TRP* 3.5 40.2 + - + -
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Residues in contact with ILE 275 (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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85A PHE* 4.5 1.6 - - + -
86A PRO* 4.2 14.8 - - + -
200A PHE* 4.0 19.3 - - + -
208A ARG* 3.5 33.4 - - + -
209A TYR 3.5 7.6 - - - +
210A CYS* 3.8 8.3 - - + -
273A ILE* 3.7 27.1 - - + -
274A GLN* 1.3 83.7 - - - +
276A HIS* 1.3 66.7 + - - +
277A GLU 4.2 0.9 - - - +
293A TRP* 3.9 3.1 - - - -
297A THR 4.5 2.3 - - - +
298A HIS* 3.0 22.9 + - - +
299A PRO 4.6 3.2 + - - -
301A PHE* 4.1 27.1 - - + -
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Residues in contact with HIS 276 (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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208A ARG* 3.3 1.2 - - - -
209A TYR* 2.9 43.3 + + + -
275A ILE* 1.3 80.4 - - - +
277A GLU* 1.3 76.9 + - - +
278A ALA 3.5 0.3 + - - -
279A SER* 5.9 0.2 - - - -
282A ASP* 3.0 39.7 + - - -
286A ILE* 4.1 18.8 - - + +
293A TRP* 3.8 25.2 - + + -
298A HIS* 2.7 33.6 - + + +
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Residues in contact with GLU 277 (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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206A LYS* 3.6 33.2 + - + +
207A VAL 3.7 11.4 - - - +
208A ARG* 3.9 25.0 + - + +
275A ILE* 4.2 2.0 - - - +
276A HIS* 1.3 89.4 + - - +
278A ALA* 1.3 75.6 + - - +
279A SER* 4.4 2.6 - - - -
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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