Contacts of the strand formed by residues 290 - 296 (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 LEU 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A GLN 3.8 1.3 - - - +
286A LEU* 3.6 4.9 - - - +
287A SER* 3.0 48.4 + - - +
288A ASN 3.8 5.8 - - - +
289A GLY* 1.4 82.0 - - - +
291A LEU* 1.3 65.2 + - - +
292A LYS* 4.8 8.7 - - + +
306A GLU* 4.1 27.1 - - + +
307A VAL 3.7 17.9 - - - +
308A GLN* 4.5 1.3 - - + +
309A VAL* 3.8 7.1 - - - +
103B ARG* 3.7 29.2 - - - +
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Residues in contact with LEU 291 (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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257A VAL* 5.7 2.7 - - + -
264A LEU* 3.6 30.5 - - + -
268A PHE* 4.3 10.8 - - + -
284A LEU* 3.7 35.9 - - + -
285A GLN 3.7 2.5 - - - +
286A LEU* 3.8 26.0 - - + -
290A LEU* 1.3 75.9 - - - +
292A LYS* 1.3 67.3 + - - +
293A ILE* 4.0 19.1 - - + -
305A GLU 3.7 1.0 - - - +
306A GLU* 3.4 1.9 - - - +
307A VAL* 2.7 44.5 + - + +
309A VAL* 3.9 11.4 - - + +
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Residues in contact with LYS 292 (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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283A ARG 3.6 1.6 - - - +
284A LEU* 3.6 3.1 - - - -
285A GLN* 2.8 62.6 + - + +
290A LEU* 4.2 10.5 - - + +
291A LEU* 1.3 73.1 - - - +
293A ILE* 1.3 62.6 + - - +
294A GLN* 5.5 1.7 - - + +
304A GLU* 3.3 35.6 + - + +
305A GLU 3.4 2.9 - - - -
306A GLU* 3.4 36.4 + - + +
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Residues in contact with ILE 293 (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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264A LEU* 5.0 0.9 - - + -
267A ALA* 3.6 31.2 - - + -
268A PHE* 3.8 24.5 - - + -
271A THR* 3.2 31.2 - - + +
282A ILE* 3.8 24.7 - - + -
283A ARG 3.5 4.7 - - - +
284A LEU* 4.9 2.5 - - + -
291A LEU* 4.0 18.8 - - + -
292A LYS* 1.3 74.4 - - - +
294A GLN* 1.3 63.8 + - - +
303A ALA 4.5 0.2 - - - -
304A GLU* 3.1 8.9 - - - +
305A GLU* 2.7 40.0 + - + +
307A VAL* 4.0 15.3 - - + -
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Residues in contact with GLN 294 (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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281A GLY 4.7 0.2 - - - +
282A ILE* 3.5 5.4 - - - -
283A ARG* 2.8 70.9 + - + +
285A GLN* 4.6 12.7 - - + +
292A LYS* 5.5 1.8 - - + +
293A ILE* 1.3 77.1 - - - +
295A ALA* 1.3 62.7 + - - +
296A ASN* 3.0 25.6 + - - +
302A GLU* 3.5 22.0 + - - +
303A ALA 3.3 9.4 - - - +
304A GLU* 3.7 21.3 - - + +
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Residues in contact with ALA 295 (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* 3.1 30.3 - - - +
274A LEU 3.8 3.1 - - - -
275A SER* 4.0 14.6 - - - +
281A GLY 4.5 4.7 - - - -
282A ILE* 3.9 18.6 - - + -
294A GLN* 1.3 75.3 - - - +
296A ASN* 1.3 63.5 + - - +
302A GLU* 3.2 8.7 - - - +
303A ALA* 2.9 32.4 + - + +
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Residues in contact with ASN 296 (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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274A LEU 3.1 8.7 - - - +
275A SER* 3.7 0.9 - - - -
276A ASN* 3.6 15.1 + - - +
281A GLY 4.8 4.5 + - - +
283A ARG* 5.3 4.0 - - - +
294A GLN* 3.0 32.1 - - - +
295A ALA* 1.3 78.1 - - - +
297A ASN* 1.3 61.2 + - - +
300A GLN* 5.0 4.9 - - - +
301A GLU 3.3 9.0 - - - +
302A GLU* 3.0 27.2 + - - +
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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