Contacts of the strand formed by residues 273 - 280 (chain A) in PDB entry 1II7
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 PHE 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLN* 3.4 24.2 - - - -
16A PHE* 3.8 24.2 - + - -
21A ARG* 3.5 21.8 - - - -
228A ARG* 3.7 33.9 - - + +
230A ASP 3.4 31.4 - - - -
231A PHE* 4.1 17.3 - + + -
234A TYR* 3.7 10.7 - - - -
235A GLU* 2.9 29.0 + - - +
236A VAL 3.6 1.7 + - - -
271A ARG* 3.7 11.6 + - - -
272A PRO* 1.3 82.1 - - - +
274A ILE* 1.3 62.1 + - - +
275A ASP 4.1 0.2 - - - -
301A TYR* 3.3 24.7 - + + -
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Residues in contact with ILE 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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231A PHE* 4.0 4.1 - - - -
235A GLU* 4.9 2.5 - - + +
236A VAL* 3.5 24.5 - - + +
238A TYR* 3.5 36.3 - - + +
272A PRO* 4.4 13.5 - - + -
273A PHE* 1.3 81.3 - - - +
275A ASP* 1.3 60.0 + - - +
276A VAL* 4.1 11.0 - - + -
295A LEU 5.4 1.3 - - - +
296A ILE* 4.6 10.3 - - + -
297A PRO* 4.8 13.2 - - + -
300A ALA* 3.9 23.3 - - + -
301A TYR 2.8 8.6 + - - +
302A VAL* 3.4 11.1 - - + +
303A ARG 3.0 24.9 + - - +
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Residues in contact with ASP 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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231A PHE* 4.0 15.5 - - + +
234A TYR* 4.0 13.8 - - + +
236A VAL 3.0 8.2 + - - +
237A ARG* 2.5 42.6 + - + -
238A TYR* 2.7 32.2 + - - +
274A ILE* 1.3 71.3 - - - +
276A VAL* 1.3 60.6 + - - +
303A ARG* 2.8 45.4 + - - +
305A ASN* 3.1 12.3 - - - +
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Residues in contact with VAL 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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237A ARG* 5.7 0.4 - - - -
238A TYR* 3.3 10.8 - - + +
245A PHE* 4.0 9.0 - - + -
274A ILE* 4.1 13.0 - - + -
275A ASP* 1.3 83.9 + - - +
277A LYS* 1.3 63.6 + - - +
278A ILE* 3.7 30.1 - - + -
292A LEU* 4.0 24.9 - - + -
296A ILE* 5.3 0.2 - - + -
302A VAL* 4.1 9.6 - - + -
303A ARG 2.8 16.6 + - - +
304A LEU* 3.6 17.7 - - + -
305A ASN* 2.8 37.8 + - - +
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Residues in contact with LYS 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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237A ARG* 5.2 17.9 - - + +
238A TYR 2.7 14.4 + - - +
239A GLU* 3.4 37.4 + - + +
240A TRP 3.0 26.5 + - - -
245A PHE* 4.2 0.3 - - - -
276A VAL* 1.3 73.7 - - - +
278A ILE* 1.3 66.7 + - - +
279A LYS* 5.6 6.3 - - - +
305A ASN* 3.7 20.6 - - + +
331A TRP* 4.5 23.5 - - - +
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Residues in contact with ILE 278 (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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240A TRP* 4.1 10.5 - - + -
245A PHE* 3.8 20.4 - - + -
276A VAL* 3.7 22.9 - - + -
277A LYS* 1.3 82.7 - - - +
279A LYS* 1.3 67.2 + - - +
285A ILE* 4.1 26.2 - - + -
288A ALA* 3.7 24.2 - - + -
289A ILE* 3.9 29.4 - - + -
292A LEU* 4.9 0.2 - - + -
304A LEU* 5.3 2.5 - - + -
305A ASN 3.2 11.6 + - - +
306A ILE* 3.4 10.6 - - + +
307A GLY 3.0 21.7 + - - +
331A TRP* 5.7 0.2 - - - -
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Residues in contact with LYS 279 (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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240A TRP* 4.3 9.1 + - - +
277A LYS* 5.6 7.0 - - - +
278A ILE* 1.3 80.6 - - - +
280A GLY* 1.3 57.4 + - - +
284A GLU* 4.2 12.8 - - - +
285A ILE* 4.6 4.9 - - - -
307A GLY* 3.4 7.9 - - - +
331A TRP* 3.5 25.4 - - + -
333A ILE* 3.2 49.3 - - + +
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Residues in contact with GLY 280 (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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279A LYS* 1.3 79.6 - - - +
281A SER* 1.3 67.4 + - - -
284A GLU* 4.5 7.2 - - - -
285A ILE* 3.5 7.3 - - - +
307A GLY 3.0 17.4 + - - +
308A TRP 4.1 0.2 - - - -
309A ARG* 3.6 14.7 + - - -
333A ILE* 3.6 9.1 - - - +
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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