Contacts of the helix formed by residues 294 - 305 (chain A) in PDB entry 2UYC
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 SER 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TYR* 5.8 0.9 - - - -
292A HIS* 3.0 22.5 + - - +
293A PRO* 1.3 77.4 - - - +
295A THR* 1.3 56.8 + - - +
296A SER* 3.5 3.3 + - - -
297A GLN* 3.2 20.7 + - - +
298A ALA* 2.8 28.9 + - - +
403C G 2.6 28.5 + - - -
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Residues in contact with THR 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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276A PRO* 4.2 21.7 - - + +
292A HIS 4.8 1.1 - - - +
293A PRO 3.5 7.0 + - - +
294A SER* 1.3 72.3 + - - +
296A SER* 1.3 58.4 + - - +
298A ALA* 3.2 7.9 + - - +
299A TYR* 2.9 46.4 + - - -
404C A 4.6 7.6 + - - -
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LYS* 4.9 2.6 - - - +
294A SER* 3.1 3.7 + - - -
295A THR* 1.3 83.1 + - - +
297A GLN* 1.3 63.8 + - - +
299A TYR* 3.5 9.3 + - - +
300A LYS* 3.2 21.0 + - - +
1338A GOL 2.8 24.3 + - - -
403C G 3.1 36.3 + - - +
404C A 3.7 18.2 - - - -
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 4.2 5.2 - - - +
44A TYR* 3.2 49.6 - - + +
292A HIS* 3.9 9.6 - - - +
294A SER* 3.1 25.3 + - - +
296A SER* 1.3 78.4 + - - +
298A ALA* 1.3 56.4 + - - +
300A LYS* 3.3 25.1 + - - +
301A GLN* 2.7 45.0 + - - +
401C T 4.8 2.7 - - - +
402C G 4.0 14.3 + - - -
403C G 2.7 23.5 + - - +
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PRO* 4.1 22.4 - - + -
291A VAL* 4.6 4.5 - - + -
292A HIS* 4.0 22.2 - - - +
294A SER 2.8 16.8 + - - +
295A THR* 3.2 6.0 + - - +
297A GLN* 1.3 78.3 - - - +
299A TYR* 1.3 61.7 + - - +
301A GLN* 3.7 11.7 + - - +
302A PHE* 3.0 35.9 + - + -
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Residues in contact with TYR 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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205A LEU* 3.7 9.2 - - - +
251A LEU* 5.7 0.2 - - - +
252A SER 3.8 4.5 - - - +
260A ALA 5.1 0.9 - - - -
261A LYS* 3.7 24.6 - - + +
262A THR* 3.6 25.1 - - + -
273A LYS* 3.6 31.6 - - + -
274A LEU 2.5 30.6 + - - -
276A PRO* 3.6 28.0 - - + +
279A CYS* 3.8 15.6 - - - -
295A THR* 2.9 36.2 + - - +
296A SER* 3.8 4.9 - - - +
298A ALA* 1.3 76.6 - - - +
300A LYS* 1.3 57.5 + - - +
302A PHE* 3.9 3.7 - - - +
303A GLY* 2.9 26.3 + - - -
1338A GOL 4.0 15.9 - - - +
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Residues in contact with LYS 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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42A ASP* 4.2 8.1 + - - -
253A ALA* 3.5 36.8 - - + +
254A TYR* 3.7 31.7 + - + -
261A LYS* 4.1 4.2 - - - +
296A SER 3.2 12.4 + - - +
297A GLN* 3.5 29.6 + - - +
299A TYR* 1.3 79.5 - - - +
301A GLN* 1.3 64.6 + - + +
303A GLY 3.1 1.4 + - - -
304A ASN* 3.1 28.2 + - - +
401C T 3.0 41.6 + - - -
402C G 5.5 0.6 + - - -
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Residues in contact with GLN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLY* 6.0 0.9 - - - -
21A LEU* 3.5 33.7 - - + +
42A ASP* 4.9 0.8 + - - +
44A TYR* 3.2 43.6 + - - +
45A ALA* 3.5 11.7 - - + +
48A VAL* 3.6 8.9 - - - +
292A HIS* 3.5 24.2 + - - +
297A GLN* 2.7 27.5 + - + +
298A ALA* 3.7 6.7 - - - +
300A LYS* 1.3 79.3 - - + +
302A PHE* 1.3 63.0 + - - +
304A ASN* 3.1 9.3 + - - +
305A SER* 3.0 21.8 + - - -
1328A SAH 4.5 1.7 + - - -
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Residues in contact with PHE 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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21A LEU* 3.3 27.8 - - + -
251A LEU* 3.9 9.9 - - + +
276A PRO* 3.7 22.2 - - + -
279A CYS* 4.0 22.4 - - + -
280A ALA* 3.5 32.1 - - + -
283A MET* 3.6 16.8 - - + +
285A TYR* 3.8 24.0 - + - -
289A TYR* 4.5 13.5 - + - -
291A VAL* 3.9 25.6 - - + -
298A ALA* 3.0 33.2 + - + +
299A TYR 4.3 2.2 - - - +
301A GLN* 1.3 76.6 - - - +
303A GLY* 1.3 62.8 + - - +
305A SER* 3.2 13.2 + - - -
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Residues in contact with GLY 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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165A ARG* 5.0 0.3 + - - -
251A LEU* 3.5 16.0 - - - +
252A SER 3.4 32.3 - - - -
253A ALA 3.8 6.9 + - - -
283A MET* 5.6 0.7 - - - +
299A TYR 2.9 10.8 + - - -
300A LYS 3.5 3.4 - - - -
301A GLN 3.1 0.4 - - - -
302A PHE* 1.3 79.3 - - - +
304A ASN* 1.3 55.8 + - - +
305A SER 3.8 0.9 + - - +
427D C 3.0 22.2 + - - +
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Residues in contact with ASN 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLN* 5.9 2.3 - - - -
119A GLU* 5.3 0.2 - - - +
253A ALA* 3.1 25.2 - - - +
254A TYR* 4.8 7.0 + - - -
300A LYS* 3.1 22.7 + - - +
301A GLN* 3.1 10.4 + - - +
303A GLY* 1.3 75.2 - - - +
305A SER* 1.3 66.2 + - - +
1328A SAH 3.7 49.0 + - + +
427D C 3.3 40.7 - - - +
428D G 4.6 0.5 + - - -
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.7 7.5 - - - +
119A GLU* 5.0 0.3 - - - +
163A ASN* 4.6 3.1 + - - -
165A ARG* 5.1 0.2 + - - -
283A MET* 3.1 19.6 - - - +
285A TYR* 2.5 33.9 + - - -
301A GLN 3.0 14.0 + - - -
302A PHE* 3.2 12.9 + - - +
303A GLY 4.6 0.7 - - - +
304A ASN* 1.3 82.9 - - - +
306A VAL* 1.3 68.3 + - - +
1328A SAH 2.9 17.9 + - - -
427D C 3.7 12.8 - - - +
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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