Contacts of the strand formed by residues 271 - 277 (chain A) in PDB entry 2UYQ
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 TRP 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TRP* 4.5 2.9 - + - -
201A PHE* 5.1 2.5 + + - -
204A ILE* 4.0 24.2 - - + -
205A GLY* 4.0 10.3 - - - -
208A SER* 3.5 24.0 - - - -
212A SER 4.2 0.9 - - - -
213A ARG* 4.1 4.3 - - - -
214A ILE* 3.8 28.3 - - + -
265A TRP* 5.0 3.8 - - - -
266A LEU* 3.1 48.7 + - + +
267A ASN* 3.4 21.0 - - - +
269A HIS* 3.5 6.8 + - + -
270A GLY* 1.3 76.7 - - - +
272A ARG* 1.3 63.8 + - - +
273A ALA 4.0 0.7 - - - -
307A ALA* 3.8 24.7 - - + -
308A HIS 3.2 8.7 - - - -
309A ARG* 3.1 58.3 - - + +
310A LEU* 4.0 12.1 - - - +
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Residues in contact with ARG 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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267A ASN* 3.5 8.1 + - - -
271A TRP* 1.3 74.8 + - - +
273A ALA* 1.3 62.4 + - - +
274A THR* 5.5 2.0 - - - +
306A THR 4.0 0.3 - - - +
307A ALA* 3.3 2.3 - - - -
308A HIS* 2.8 47.5 + - + +
310A LEU* 3.5 40.5 - - + +
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Residues in contact with ALA 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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263A ALA* 3.8 27.5 - - - +
266A LEU* 3.8 12.3 - - + -
267A ASN* 2.7 32.5 + - - +
272A ARG* 1.3 75.8 - - - +
274A THR* 1.3 67.1 + - - +
305A VAL* 4.2 4.7 - - + -
306A THR 3.4 4.7 - - - +
307A ALA* 3.6 17.7 - - + -
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Residues in contact with THR 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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263A ALA* 4.9 2.5 - - - -
272A ARG* 5.5 1.7 + - - +
273A ALA* 1.3 77.1 + - - +
275A ALA* 1.3 72.0 + - - +
304A PHE 4.1 0.2 - - - +
305A VAL* 3.3 6.4 - - - +
306A THR* 2.9 35.5 + - - -
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Residues in contact with ALA 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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263A ALA* 4.6 9.1 - - + +
274A THR* 1.3 85.6 - - - +
276A GLN* 1.3 61.4 + - - +
277A SER 4.2 0.8 + - - -
303A GLU* 3.7 30.3 - - + +
304A PHE 3.6 4.0 - - - +
305A VAL* 3.9 14.8 - - + -
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Residues in contact with GLN 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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90A PHE* 4.4 17.0 - - + -
275A ALA* 1.3 74.7 - - - +
277A SER* 1.3 68.7 + - - +
280A ASP* 3.9 18.0 + - - +
281A GLU* 2.9 49.4 + - + +
284A ARG* 4.4 10.1 - - - +
303A GLU* 4.5 2.0 - - - -
304A PHE* 2.7 43.4 + - + +
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Residues in contact with SER 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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275A ALA 4.2 1.2 + - - -
276A GLN* 1.3 78.0 + - - +
278A ALA* 1.3 65.6 + - - +
279A PRO* 3.6 11.4 - - - +
280A ASP* 3.2 34.2 + - - +
281A GLU* 3.0 21.1 + - - +
298A LYS* 5.6 10.2 - - - +
302A ALA 4.6 0.4 - - - -
303A GLU* 4.0 26.2 + - - +
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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