Contacts of the strand formed by residues 296 - 304 (chain A) in PDB entry 3I5D
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 ASN 296 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PHE* 5.3 0.4 - - - -
292A ALA* 6.0 5.3 - - - +
293A PRO 5.3 4.2 + - - -
295A TYR* 1.3 87.6 - - - +
297A PHE* 1.3 71.0 + - - +
298A ARG* 5.5 1.0 + - - +
316A LYS* 3.2 37.7 - - - +
317A GLY 3.0 16.6 - - - +
318A TYR* 3.6 24.2 - - + +
70B LYS* 5.8 4.2 - - - +
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Residues in contact with PHE 297 (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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95A PRO* 3.6 22.9 - - + -
96A PRO* 5.5 0.2 - - + -
103A PHE* 3.4 44.6 - + + -
295A TYR* 4.3 18.4 - + - -
296A ASN* 1.3 82.1 - - - +
298A ARG* 1.3 77.0 + - - +
299A PHE* 3.1 28.7 - + + -
315A ILE 3.6 0.3 - - - +
316A LYS* 3.7 0.9 - - - -
317A GLY* 3.0 29.3 + - - +
97B GLN* 4.4 30.3 - - + -
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Residues in contact with ARG 298 (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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145A ASP* 5.9 5.7 - - - +
171A GLU* 2.7 43.5 + - - +
296A ASN* 5.5 0.4 - - - +
297A PHE* 1.3 87.5 - - - +
299A PHE* 1.3 65.7 + - - +
314A LEU* 3.9 27.5 - - + +
315A ILE 3.3 5.6 - - - +
316A LYS* 3.7 33.3 - - + +
88B ASP* 6.1 0.4 - - - -
90B ALA* 4.3 35.0 - - + +
91B ASP* 4.5 4.4 - - + -
97B GLN* 4.2 12.0 + - - +
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Residues in contact with PHE 299 (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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87A TRP* 6.5 0.2 - + - -
92A TYR* 6.0 3.8 - + - -
95A PRO* 3.8 27.1 - - + -
105A LEU* 4.5 13.9 - - + -
297A PHE* 3.1 33.4 - + + -
298A ARG* 1.3 75.6 - - - +
300A ALA* 1.3 69.4 - - - +
301A LYS* 4.8 8.3 - - + -
314A LEU* 3.5 4.3 - - - +
315A ILE* 2.9 76.5 + - + +
317A GLY* 4.8 9.2 - - - -
91B ASP* 4.4 9.2 - - - +
97B GLN* 4.6 11.9 - - - +
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Residues in contact with ALA 300 (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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299A PHE* 1.3 82.3 - - - +
301A LYS* 1.3 71.3 + - - +
302A TYR* 3.7 37.7 - - + +
312A ARG* 3.9 22.4 - - - +
313A THR 3.3 12.1 - - - +
314A LEU* 4.6 0.9 - - - -
91B ASP* 4.5 5.5 + - + +
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Residues in contact with LYS 301 (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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92A TYR* 2.7 39.0 + - - -
299A PHE* 4.8 7.9 - - + -
300A ALA* 1.3 83.2 - - - +
302A TYR* 1.3 62.8 + - - +
303A TYR* 3.3 26.7 + - + +
312A ARG* 3.1 5.5 - - - -
313A THR* 2.9 41.1 + - + +
315A ILE* 4.5 16.2 - - + +
302C TYR* 3.2 39.4 - - + -
310C GLU* 3.7 10.7 + - - -
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Residues in contact with TYR 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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167A TRP* 4.3 0.7 - + - -
300A ALA* 3.7 30.5 - - + +
301A LYS* 1.3 74.8 - - - +
303A TYR* 1.3 70.9 + - - +
310A GLU* 4.0 24.7 - - - +
311A THR 3.7 2.5 - - - +
312A ARG* 3.6 33.5 + - + -
91B ASP 3.7 7.3 + - - -
92B TYR* 3.5 51.7 - + - +
301B LYS* 3.2 31.4 - - + -
302B TYR 4.4 2.3 - - - +
303B TYR* 3.8 17.1 - - + -
302C TYR 4.3 5.7 - - - +
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Residues in contact with TYR 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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301A LYS* 3.3 33.9 + - + +
302A TYR* 1.3 90.8 - - - +
304A LYS* 1.3 62.0 + - - +
305A ASN* 3.0 8.7 + - - +
310A GLU* 4.0 3.2 - - - +
311A THR* 2.8 46.9 + - - +
312A ARG* 4.9 0.9 - - - -
313A THR* 3.6 23.7 + - - -
303B TYR* 4.1 3.1 - - - -
302C TYR* 3.8 22.1 - - + +
303C TYR* 4.1 1.3 - - - -
304C LYS* 3.3 48.9 - - + +
310C GLU* 2.9 27.8 + - + -
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Residues in contact with LYS 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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303A TYR* 1.3 69.1 - - - +
305A ASN* 1.3 69.4 + - - +
306A SER* 3.7 1.0 + - - -
308A GLY* 5.5 5.6 - - - +
309A THR 4.2 4.5 - - - -
310A GLU* 5.0 4.7 - - + +
303B TYR* 3.3 48.9 - - + +
304B LYS 5.4 3.5 - - - +
304C LYS 5.3 4.9 - - - +
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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