Contacts of the strand formed by residues 301 - 308 (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 TYR 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.7 34.8 - + - -
18A LYS* 3.1 27.3 - - + +
20A GLN* 4.9 6.4 + - - +
21A ARG* 3.6 28.6 + - + +
231A PHE* 3.7 10.6 - - + -
271A ARG* 3.4 41.2 + - - -
272A PRO 3.1 5.5 + - - -
273A PHE* 3.3 25.9 - + + -
274A ILE* 2.8 25.8 + - - +
300A ALA* 1.3 81.9 - - - +
302A VAL* 1.3 59.8 + - - +
324A GLU* 3.8 11.4 + - + +
325A TYR* 3.4 25.6 - + + +
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Residues in contact with VAL 302 (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* 3.7 6.5 - - - -
274A ILE* 3.4 17.5 - - + +
276A VAL* 4.1 8.3 - - + -
296A ILE* 3.9 24.9 - - + -
300A ALA* 4.3 3.1 - - + +
301A TYR* 1.3 81.4 - - - +
303A ARG* 1.3 57.9 + - - +
304A LEU* 3.8 28.0 - - + -
321A LEU* 5.3 0.9 - - + -
323A VAL* 3.9 27.1 - - + -
325A TYR 2.8 11.4 + - - +
326A LEU* 3.2 15.4 - - + -
327A LYS 2.7 32.6 + - - +
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Residues in contact with ARG 303 (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* 3.3 56.7 - - + +
232A GLY* 4.2 3.8 - - - +
237A ARG* 4.3 7.3 - - - +
274A ILE 3.0 7.1 + - - +
275A ASP* 2.8 38.1 + - - +
276A VAL* 2.8 31.0 + - - +
302A VAL* 1.3 74.6 - - - +
304A LEU* 1.3 66.1 + - - +
305A ASN* 3.7 18.4 + - - +
327A LYS* 3.2 16.3 - - + +
329A ASP* 3.5 26.9 + - - +
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Residues in contact with LEU 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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276A VAL* 3.6 28.9 - - + -
278A ILE* 5.3 2.0 - - + -
289A ILE* 4.0 8.5 - - + -
292A LEU* 4.0 14.6 - - + -
302A VAL* 3.8 16.6 - - + -
303A ARG* 1.3 73.5 - - - +
305A ASN* 1.3 57.3 + - - +
306A ILE* 3.7 18.4 - - + -
317A ILE* 3.8 20.6 - - + -
321A LEU* 3.7 22.7 - - + -
326A LEU* 3.7 15.9 - - + -
327A LYS 2.8 11.2 + - - +
328A ILE* 3.4 11.2 - - + +
329A ASP* 2.7 34.1 + - - +
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Residues in contact with ASN 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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237A ARG* 5.1 2.4 + - - +
275A ASP* 3.1 22.8 - - - +
276A VAL 2.8 27.7 + - - +
277A LYS* 3.7 17.3 - - + +
278A ILE* 3.2 25.3 + - - +
303A ARG* 3.7 28.8 + - - +
304A LEU* 1.3 72.5 - - - +
306A ILE* 1.3 61.2 + - - +
329A ASP* 3.4 17.8 + - + +
331A TRP* 4.8 12.1 + - + +
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Residues in contact with ILE 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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278A ILE* 3.4 11.7 - - + +
285A ILE* 3.5 35.9 - - + -
289A ILE* 5.8 1.1 - - + -
304A LEU* 4.2 24.9 - - + -
305A ASN* 1.3 77.4 - - - +
307A GLY* 1.3 63.4 - - - +
308A TRP* 3.6 14.7 + - + +
312A PHE* 4.9 0.7 - - + -
314A LEU* 4.6 8.3 - - + -
317A ILE* 4.4 20.4 - - + -
328A ILE* 4.0 21.5 - - + -
329A ASP 2.7 13.8 + - - +
330A THR* 3.1 9.3 - - + +
331A TRP* 2.9 28.4 + - - +
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Residues in contact with GLY 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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278A ILE 3.0 11.5 + - - +
279A LYS* 3.4 2.3 - - - -
280A GLY 3.0 28.6 + - - +
285A ILE* 4.1 2.1 - - - +
305A ASN 4.0 0.2 + - - -
306A ILE* 1.3 73.2 - - - +
308A TRP* 1.3 58.8 + - - -
331A TRP* 3.1 40.2 - - - +
333A ILE* 3.2 6.6 - - - +
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Residues in contact with TRP 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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280A GLY 3.7 3.8 - - - -
285A ILE* 4.3 1.3 - - + -
306A ILE* 3.6 9.1 + - + -
307A GLY* 1.3 75.5 - - - +
309A ARG* 1.3 67.6 + - - +
310A LYS 3.7 13.2 - - - +
311A PRO* 3.4 27.8 - - + +
312A PHE* 3.5 57.9 - + + -
314A LEU* 3.8 24.5 - - + -
330A THR* 3.4 38.7 + - + -
331A TRP 3.1 12.8 + - - -
332A ARG* 3.4 22.0 - - + +
333A ILE* 3.2 21.2 + - - -
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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