Contacts of the strand formed by residues 302 - 308 (chain A) in PDB entry 4TR8
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 GLU 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A LEU* 3.4 5.8 - - - +
294A GLN* 3.5 27.5 + - + +
295A ALA 3.2 13.0 - - - +
296A ASN* 3.0 22.4 + - - +
300A GLN 3.8 3.5 + - - +
301A GLU* 1.3 74.7 - - - +
303A ALA* 1.3 69.9 + - - +
304A GLU* 5.0 10.7 - - - +
105B ARG 4.0 0.7 - - - +
106B PHE* 3.3 3.1 - - - -
107B THR* 2.8 48.2 + - + +
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Residues in contact with ALA 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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271A THR* 3.6 36.3 - - + +
274A LEU* 4.0 8.7 - - + +
293A ILE 4.5 0.2 - - - -
294A GLN* 3.3 5.9 - - - +
295A ALA 2.9 31.2 + - - +
302A GLU* 1.3 74.8 - - - +
304A GLU* 1.3 61.6 + - - +
105B ARG 3.3 4.7 - - - -
106B PHE* 3.7 24.5 - - + -
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 4.3 2.3 - - - +
285A GLN* 5.2 0.2 - - - +
292A LYS* 3.3 36.9 + - + +
293A ILE 3.1 12.3 - - - +
294A GLN* 3.7 22.5 - - + +
302A GLU* 5.0 10.5 - - - +
303A ALA* 1.3 76.0 - - - +
305A GLU* 1.3 66.8 + - - +
306A GLU* 5.7 2.5 - - + -
103B ARG 3.9 0.6 - - - +
104B SER* 3.4 2.1 - - - -
105B ARG* 2.8 60.3 + - + +
106B PHE* 5.5 1.0 - - - -
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Residues in contact with GLU 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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263A GLN* 5.1 3.1 + - - +
267A ALA* 3.5 28.7 - - + +
270A ARG* 2.7 45.4 + - - +
271A THR* 3.8 13.9 - - + +
291A LEU 3.7 1.0 - - - +
292A LYS* 3.4 2.5 - - - -
293A ILE* 2.7 41.1 + - + +
304A GLU* 1.3 75.9 - - - +
306A GLU* 1.3 73.2 + - - +
307A VAL* 4.3 4.5 - - - +
103B ARG* 3.4 12.4 - - + +
104B SER* 3.1 20.6 + - - +
106B PHE* 5.5 0.3 - - - -
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Residues in contact with GLU 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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263A GLN* 5.3 1.9 + - - -
290A LEU* 4.1 17.1 - - + +
291A LEU 3.4 3.6 - - - -
292A LYS* 3.4 40.0 + - + -
304A GLU* 5.7 3.1 - - + +
305A GLU* 1.3 77.9 - - - +
307A VAL* 1.3 63.8 + - - +
308A GLN 4.3 0.2 - - - -
103B ARG* 2.7 74.3 + - - +
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Residues in contact with VAL 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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260A ASP 5.8 1.3 - - - +
263A GLN* 3.6 33.2 - - + +
264A LEU* 3.9 26.9 - - + -
267A ALA* 3.7 29.6 - - + -
290A LEU* 3.7 4.4 - - - +
291A LEU* 2.7 42.4 + - + +
293A ILE* 4.0 10.3 - - + -
305A GLU* 4.3 7.4 - - + +
306A GLU* 1.3 79.5 - - - +
308A GLN* 1.3 74.9 + - - +
309A VAL* 4.5 1.3 - - + -
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Residues in contact with GLN 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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259A GLY* 5.1 2.9 - - - -
260A ASP 5.3 1.6 + - - -
263A GLN* 4.4 9.9 - - - +
289A GLY 3.5 13.4 + - - +
290A LEU* 4.6 3.6 - - + -
307A VAL* 1.3 80.2 - - - +
309A VAL* 1.3 63.9 + - - +
103B ARG* 3.4 30.1 + - - +
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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