Contacts of the helix formed by residues 300 - 306 (chain A) in PDB entry 1UWV
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 PHE 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A MSE 3.7 22.9 - - + -
275A VAL* 3.8 27.4 - - + -
278A ALA* 3.6 27.1 - - + -
279A LEU* 4.6 3.6 - - + +
292A ASP* 3.6 13.6 + - - +
295A CYS 5.2 0.6 + - - -
298A GLY 3.3 0.2 - - - -
299A ASN* 1.3 92.3 - - + +
301A THR* 1.3 64.8 + - - +
302A LEU 3.4 1.3 - - - -
303A PRO* 3.4 4.2 - - - +
304A LEU* 3.1 31.5 + - + +
361A LEU* 3.5 34.3 - - + -
363A ASP* 3.8 25.4 - - + -
387A VAL* 3.7 19.7 - - + -
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Residues in contact with THR 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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292A ASP* 2.3 30.5 + - + +
295A CYS* 3.3 14.2 - - - +
298A GLY* 3.1 16.2 + - - -
300A PHE* 1.3 76.1 - - - +
302A LEU* 1.3 62.8 + - - +
304A LEU* 3.4 8.8 + - - +
305A ALA* 3.2 20.4 + - - +
311A VAL* 3.6 22.5 - - + +
313A GLY* 4.2 12.1 - - - -
336A VAL* 3.8 17.3 - - + -
338A PHE* 4.0 12.1 - - + -
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Residues in contact with LEU 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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254A LEU* 3.5 15.0 - - + -
256A LEU* 3.9 15.3 - - + -
297A MSE 4.2 9.0 - - - +
298A GLY* 3.1 9.6 + - - +
301A THR* 1.3 75.4 - - - +
303A PRO* 1.3 73.3 - - + +
305A ALA* 3.1 14.7 + - - +
306A THR* 3.4 9.5 + - - +
324A GLY 4.1 2.9 - - - +
327A ASN* 3.7 31.9 - - + +
328A ALA* 3.9 22.0 - - + +
331A ASN* 5.2 0.4 - - - +
333A LEU* 3.6 18.4 - - + +
336A VAL* 4.1 8.3 - - + -
338A PHE* 3.6 32.3 - - + -
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Residues in contact with PRO 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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251A SER 5.5 0.4 - - - +
252A ASN* 4.2 18.8 - - + +
254A LEU* 3.7 17.0 - - + -
256A LEU* 6.4 1.1 - - + -
275A VAL* 3.8 16.2 - - + -
279A LEU* 3.7 25.5 - - + +
298A GLY 3.7 0.7 - - - +
299A ASN 3.4 26.7 - - - +
300A PHE 3.4 6.5 - - - +
302A LEU* 1.3 95.8 - - + +
304A LEU* 1.3 59.1 + - - +
306A THR* 2.7 27.9 + - + +
307A GLN* 3.9 1.7 - - - +
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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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279A LEU* 3.8 23.7 - - + +
282A LEU* 3.9 22.9 - - + -
284A VAL* 3.9 18.7 - - + +
290A VAL* 3.8 21.8 - - + -
292A ASP* 4.2 15.7 - - + -
300A PHE* 3.1 37.3 + - + +
301A THR* 3.5 10.1 - - - +
302A LEU 3.3 0.2 - - - -
303A PRO* 1.3 74.2 - - - +
305A ALA* 1.3 57.3 + - - +
307A GLN* 3.0 20.8 + - - +
308A ALA* 3.0 16.3 + - - +
311A VAL* 3.8 12.8 - - + -
361A LEU* 4.7 9.0 - - + -
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Residues in contact with ALA 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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301A THR 3.2 9.8 + - - +
302A LEU* 3.1 11.9 + - - +
304A LEU* 1.3 78.2 - - - +
306A THR* 1.3 62.5 + - - +
307A GLN 3.1 1.0 + - - -
308A ALA 3.8 1.7 - - - +
311A VAL* 3.5 17.4 - - + +
333A LEU* 4.5 9.2 - - + +
335A ASN* 2.9 42.8 + - - +
336A VAL* 4.0 18.2 - - + -
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Residues in contact with THR 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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252A ASN 6.0 0.7 - - - +
254A LEU* 4.1 20.2 - - + -
279A LEU* 5.1 0.9 - - - +
302A LEU 3.7 13.5 - - - +
303A PRO* 2.7 19.9 + - + +
304A LEU 3.2 0.6 - - - -
305A ALA* 1.3 76.1 - - - +
307A GLN* 1.3 65.5 + - - +
333A LEU* 4.0 17.7 - - + -
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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