Contacts of the strand formed by residues 301 - 307 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B PHE* 3.7 21.5 - + - -
18B LYS* 3.4 16.5 - - + +
20B GLN* 3.1 21.5 + - - +
21B ARG* 3.6 36.4 - - + +
231B PHE* 3.6 10.5 - - + -
271B ARG* 3.5 31.9 - - - -
272B PRO 3.0 5.1 + - - -
273B PHE* 3.3 25.2 - + + -
274B ILE 2.9 24.4 + - - -
300B ALA* 1.3 80.7 - - - +
302B VAL* 1.3 60.6 + - - +
324B GLU* 3.6 14.4 - - + -
325B TYR* 3.6 35.4 - + + -
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B PHE* 3.6 7.3 - - - -
274B ILE* 3.3 16.4 - - + +
276B VAL* 4.2 8.5 - - + -
292B LEU* 5.3 0.2 - - + -
296B ILE* 4.0 32.1 - - + -
300B ALA* 4.3 3.8 - - + +
301B TYR* 1.3 80.3 - - - +
303B ARG* 1.3 64.2 + - - +
304B LEU* 3.9 26.9 - - + -
321B LEU* 4.9 4.5 - - + -
323B VAL* 4.0 16.8 - - + -
325B TYR 3.1 7.4 + - - +
326B LEU* 3.5 16.7 - - + +
327B LYS* 2.8 26.3 + - - +
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B PHE* 3.4 47.5 - - + +
232B GLY* 4.7 3.6 - - - +
274B ILE 2.9 8.1 + - - -
275B ASP* 2.7 41.2 + - - +
276B VAL* 2.7 35.0 + - - +
302B VAL* 1.3 76.5 - - - +
304B LEU* 1.3 61.9 + - - +
305B ASN* 5.0 5.0 - - - +
327B LYS* 3.2 36.7 - - + +
329B ASP* 3.9 16.7 + - + +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B VAL* 3.5 17.5 - - + -
278B ILE* 4.8 2.0 - - + -
289B ILE* 4.4 6.7 - - + -
292B LEU* 3.8 28.7 - - + -
302B VAL* 3.9 10.1 - - + -
303B ARG* 1.3 72.8 - - - +
305B ASN* 1.3 60.4 + - - +
306B ILE* 3.6 19.7 + - + -
317B ILE* 3.7 20.4 - - + -
321B LEU* 3.6 21.5 - - + -
326B LEU* 3.6 17.7 - - + -
327B LYS 2.8 10.5 + - - +
328B ILE* 3.4 16.3 - - + +
329B ASP* 2.9 25.8 + - - +
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Residues in contact with ASN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B ASP* 5.7 2.0 - - - +
276B VAL 2.6 16.9 + - - +
277B LYS* 3.6 26.4 - - + +
278B ILE* 3.0 27.5 + - - +
303B ARG* 3.9 6.9 + - + +
304B LEU* 1.3 71.6 - - - +
306B ILE* 1.3 56.8 + - - +
307B GLY 3.6 0.2 + - - -
329B ASP* 3.8 11.1 - - + +
330B THR* 3.7 23.0 + - - -
331B TRP* 4.2 19.7 + - - +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ILE* 3.5 16.4 - - + +
285B ILE* 3.2 36.8 - - + -
304B LEU* 4.2 23.3 - - + -
305B ASN* 1.3 71.6 - - - +
307B GLY* 1.3 62.5 + - - +
308B TRP* 3.5 17.7 + - + -
312B PHE* 5.0 0.9 - - + -
314B LEU* 4.2 14.6 - - + -
317B ILE* 3.9 27.8 - - + -
328B ILE* 4.2 13.7 - - + -
329B ASP 3.2 11.8 + - - +
330B THR* 3.2 27.9 + - - -
331B TRP* 4.6 0.7 - - - -
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Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ILE 2.7 14.9 + - - -
279B LYS* 3.6 4.6 - - - +
280B GLY 3.5 26.9 + - - +
285B ILE* 4.0 2.6 - - - +
305B ASN 3.6 1.8 + - - -
306B ILE* 1.3 72.1 - - - +
308B TRP* 1.3 59.1 + - - +
331B TRP* 3.1 38.7 - - - +
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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