Contacts of the strand formed by residues 303 - 309 (chain A) in PDB entry 2UYO
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 GLU 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A VAL 3.5 1.0 - - - +
217A GLU* 3.5 4.3 - - - -
218A THR* 2.8 47.6 + - + +
261A VAL* 5.6 5.5 - - - +
275A ALA* 3.5 28.0 - - + +
276A GLN 3.6 9.0 - - - +
277A SER* 4.0 21.2 + - - +
278A ALA 4.2 0.2 - - - +
298A LYS 6.0 1.1 - - - +
301A PHE 4.8 3.1 - - - +
302A ALA* 1.3 77.4 - - - +
304A PHE* 1.3 65.3 + - - +
305A VAL* 3.9 3.3 - - + +
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Residues in contact with PHE 304 (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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83A TYR* 3.6 22.9 - + - -
86A VAL* 4.5 4.7 - - + -
87A ARG* 3.9 37.9 - - + -
90A PHE* 3.6 47.7 - + + -
91A PHE* 4.0 11.7 - + + -
216A VAL 3.5 4.3 - - - -
217A GLU* 4.1 11.0 - - + -
274A THR 4.1 0.3 - - - +
275A ALA* 3.7 0.5 - - - -
276A GLN* 2.7 38.8 + - - +
278A ALA* 3.9 22.2 - - + -
281A GLU* 4.1 27.4 - - + -
302A ALA* 4.7 0.2 - - + -
303A GLU* 1.3 78.5 - - - +
305A VAL* 1.3 61.8 + - - +
306A THR* 4.0 1.2 + - - -
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Residues in contact with VAL 305 (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 ILE* 3.8 1.5 - - + +
215A ALA* 3.1 6.1 - - - +
216A VAL* 2.9 37.9 + - + +
218A THR* 3.7 24.2 - - + -
262A VAL* 4.2 12.6 - - + -
263A ALA* 4.3 12.1 - - + +
266A LEU* 4.2 26.2 - - + -
273A ALA* 4.3 8.1 - - + -
274A THR 3.3 10.3 - - - +
275A ALA* 3.8 22.9 - - + -
303A GLU* 4.6 3.8 - - + +
304A PHE* 1.3 74.0 - - - +
306A THR* 1.3 69.9 + - - +
307A ALA 4.9 0.2 - - - +
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Residues in contact with THR 306 (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* 3.7 25.5 - - - -
94A TYR* 4.1 23.2 - - + -
214A ILE 3.3 10.1 - - - +
215A ALA* 4.3 3.3 - - - +
272A ARG 4.0 0.7 - - - +
273A ALA* 3.4 0.7 - - - -
274A THR* 2.9 37.5 + - - +
304A PHE 4.0 0.8 + - - -
305A VAL* 1.3 77.5 + - - +
307A ALA* 1.3 64.2 + - - +
308A HIS* 4.2 23.6 - - + +
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Residues in contact with ALA 307 (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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213A ARG* 3.1 9.9 - - - +
214A ILE* 2.9 48.9 + - + -
266A LEU* 4.0 7.0 - - + -
271A TRP* 3.9 15.9 - - + -
272A ARG 3.2 5.8 - - - +
273A ALA* 3.5 24.0 - - + -
306A THR* 1.3 75.1 - - - +
308A HIS* 1.3 65.3 + - - +
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Residues in contact with HIS 308 (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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211A GLY* 5.6 3.1 + - - +
212A SER 3.4 5.3 + - - +
213A ARG* 3.8 41.3 + - + +
271A TRP* 3.3 5.6 - - - -
272A ARG* 2.8 46.7 + - + +
306A THR* 4.2 18.3 - - + +
307A ALA* 1.3 77.4 + - - +
309A ARG* 1.3 63.9 + - - +
310A LEU* 3.5 4.1 + - + +
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Residues in contact with ARG 309 (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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205A GLY* 3.5 31.8 + - - -
208A SER* 3.8 13.2 + - - +
209A ALA 3.5 26.7 - - - +
210A VAL* 3.7 2.8 - - - +
211A GLY* 3.0 23.9 + - - +
212A SER* 2.9 18.6 + - - +
269A HIS 2.8 27.3 + - - -
270A GLY* 3.5 16.0 + - - -
271A TRP* 3.1 43.8 - - + +
308A HIS* 1.3 71.7 - - - +
310A LEU* 1.3 72.1 + - - +
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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