Contacts of the strand formed by residues 271 - 277 (chain A) in PDB entry 5U2H
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 PRO 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A ASN* 5.1 8.3 - - + -
256A ILE* 4.2 6.3 - - + -
257A TYR 4.0 3.8 - - - +
258A TRP* 3.4 39.9 - - + -
269A CYS 4.5 1.6 - - - +
270A ARG* 1.3 87.3 - - + +
272A LYS* 1.3 60.3 + - - +
273A TYR* 3.4 38.4 - - + +
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Residues in contact with LYS 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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256A ILE* 3.2 8.0 - - - +
257A TYR* 2.9 52.1 + - + +
270A ARG 3.4 3.0 + - - +
271A PRO* 1.3 72.1 - - - +
273A TYR* 1.3 62.5 + - - +
274A SER* 3.8 1.8 + - - -
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Residues in contact with TYR 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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192A ILE* 5.6 2.7 + - + -
207A ASN* 4.7 12.0 - - - +
218A PHE* 4.3 14.0 - + + -
224A PRO* 4.5 17.7 - - + -
225A GLN* 5.4 4.2 + - - -
226A CYS 5.8 0.4 - - - -
227A PRO* 5.1 11.4 - - + +
229A PHE* 3.3 37.6 - + - -
254A ILE* 4.8 8.1 - - + -
255A GLU 3.8 2.9 - - - -
256A ILE* 4.2 27.1 - - + +
271A PRO* 3.4 43.0 - - + +
272A LYS* 1.3 72.0 - - - +
274A SER* 1.3 59.2 + - - +
275A PHE* 3.8 21.7 - - + -
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Residues in contact with SER 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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254A ILE* 4.2 0.7 - - - +
255A GLU* 2.8 53.8 + - - +
256A ILE* 5.1 0.2 - - - -
257A TYR* 5.1 7.5 + - - +
272A LYS* 3.8 3.4 + - - -
273A TYR* 1.3 71.9 - - - +
275A PHE* 1.3 68.6 + - - +
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Residues in contact with PHE 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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218A PHE* 3.8 20.6 - + - -
229A PHE* 3.7 27.4 - + - -
234A ILE* 3.4 52.7 - - + +
237A GLU* 4.2 32.0 - - + +
238A THR* 5.0 9.8 - - - +
252A MET* 4.6 2.0 - - + -
253A GLY 4.3 2.7 - - - -
254A ILE* 4.1 22.2 - - + -
255A GLU* 5.8 0.2 - - - -
273A TYR* 3.8 24.0 - - + -
274A SER* 1.3 80.2 - - - +
276A ARG* 1.3 63.9 + - - +
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Residues in contact with ARG 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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238A THR* 4.6 4.3 - - - -
252A MET* 3.0 17.5 - - - +
253A GLY* 3.2 18.2 + - - +
255A GLU* 5.5 5.7 - - + +
274A SER 4.5 0.2 + - - -
275A PHE* 1.3 76.7 - - - +
277A ARG* 1.3 64.1 + - - +
278A LEU* 3.7 0.9 + - - +
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Residues in contact with ARG 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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235A PHE* 5.8 0.7 - - + -
238A THR* 3.7 21.1 + - + +
240A ASP* 4.3 13.0 - - - +
252A MET* 3.5 16.4 - - + -
276A ARG* 1.3 74.5 - - - +
278A LEU* 1.3 62.3 + - - +
279A ASP* 3.2 22.6 - - - +
281A LYS* 4.3 10.3 - - - +
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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