Contacts of the helix formed by residues 361 - 370 (chain D) in PDB entry 1UDY
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 PRO 361 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269D ARG* 4.3 14.1 - - - +
273D GLU* 3.9 37.0 - - + +
351D PHE* 4.6 10.1 - - + -
359D GLU 4.7 0.9 - - - +
360D TYR* 1.3 94.1 - - + +
362D VAL* 1.3 64.0 + - - +
363D GLU 3.5 0.2 - - - -
364D LYS* 3.4 21.2 + - + +
365D LEU* 3.6 13.9 + - + +
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Residues in contact with VAL 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D GLU* 4.1 13.0 - - + -
344D ALA 4.9 0.3 - - - +
347D ALA* 3.9 20.2 - - + +
348D VAL* 3.8 20.0 - - + +
351D PHE* 3.3 42.8 - - + -
355D GLY* 3.7 29.8 - - - +
360D TYR* 3.5 6.5 - - + -
361D PRO* 1.3 71.8 - - - +
363D GLU* 1.3 67.6 + - - +
365D LEU* 3.0 23.9 + - + +
366D MET 3.3 8.5 + - - -
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Residues in contact with GLU 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C MET* 3.7 35.1 - - + +
43D ASP* 4.7 0.7 - - - +
348D VAL* 4.3 7.0 - - - -
355D GLY 3.5 16.4 - - - +
356D PHE 4.6 0.9 - - - +
357D ASN 3.6 23.1 - - - +
358D THR* 3.7 26.2 + - - +
360D TYR 4.1 6.2 + - - +
362D VAL* 1.3 81.3 - - - +
364D LYS* 1.3 67.9 + - - +
366D MET* 3.4 4.6 + - - +
367D ARG* 2.9 60.0 + - - +
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Residues in contact with LYS 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ALA* 3.9 16.6 - - + +
40D ALA* 4.9 7.2 - - + -
43D ASP* 3.5 35.7 - - + +
90D GLY 4.7 1.6 + - - -
91D CYS* 3.3 36.9 - - - +
217D GLN* 6.2 0.9 - - - +
360D TYR 5.4 0.7 - - - +
361D PRO* 3.4 12.9 + - + +
362D VAL 3.1 0.4 - - - -
363D GLU* 1.3 82.2 - - - +
365D LEU* 1.3 74.1 + - + +
366D MET 3.1 0.4 - - - -
367D ARG* 3.1 25.6 + - - +
368D ASP* 2.9 54.0 + - - +
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Residues in contact with LEU 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D LEU* 3.4 32.8 - - + +
269D ARG* 3.9 30.1 - - + +
270D ALA* 3.9 27.4 - - + -
273D GLU* 4.7 3.8 - - + -
344D ALA* 3.7 13.4 - - + +
347D ALA* 6.2 0.2 - - + -
361D PRO* 3.7 18.8 - - + +
362D VAL* 3.0 21.2 + - + +
364D LYS* 1.3 91.1 - - + +
366D MET* 1.3 54.7 + - - +
368D ASP* 4.5 4.5 - - - +
369D ALA* 3.0 30.7 + - - +
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Residues in contact with MET 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C MET* 4.3 15.3 - - + -
341C ASN* 4.8 4.9 - - - +
366C MET* 4.2 31.2 - - + +
370C LYS* 3.9 32.8 - - + -
341D ASN* 5.0 2.5 + - - +
344D ALA* 3.7 10.0 - - + +
345D THR* 3.8 41.3 - - - +
348D VAL* 4.0 15.7 - - + -
362D VAL 3.3 8.0 + - - +
363D GLU 3.6 9.2 - - - +
364D LYS 3.1 0.6 - - - -
365D LEU* 1.3 78.2 - - - +
367D ARG* 1.3 62.8 + - - +
368D ASP 3.5 0.3 + - - -
369D ALA* 3.8 6.2 + - - +
370D LYS* 3.9 12.1 + - - +
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Residues in contact with ARG 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C MET* 4.3 10.3 - - - +
356C PHE* 3.4 16.1 - - - -
367C ARG* 3.9 24.0 - - + +
43D ASP* 3.1 37.6 + - - -
215D MET* 3.1 54.9 + - + +
216D GLY* 3.3 14.7 + - - -
218D ARG* 3.3 21.3 - - - +
358D THR* 5.4 0.6 + - - -
363D GLU* 2.9 45.8 + - - +
364D LYS* 3.1 15.6 + - - +
366D MET* 1.3 79.2 - - - +
368D ASP* 1.3 63.7 + - - +
370D LYS 4.1 1.4 + - - -
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Residues in contact with ASP 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ASP* 5.0 2.1 - - - +
92D THR* 3.5 25.0 + - - +
93D GLY 5.3 0.4 - - - -
216D GLY* 3.3 6.8 - - - -
217D GLN* 2.6 35.1 + - + +
266D LEU* 4.0 7.6 - - + +
364D LYS* 2.9 54.6 + - - +
365D LEU* 3.9 7.2 - - - +
367D ARG* 1.3 78.2 - - - +
369D ALA* 1.3 65.6 + - - +
370D LYS 3.2 0.7 + - - -
371D ILE* 3.1 26.5 + - - +
372D TYR* 4.2 0.9 - - - -
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Residues in contact with ALA 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D LEU* 3.5 17.2 - - + +
337D ALA 4.8 0.2 - - - +
340D ALA* 3.8 26.9 - - + +
341D ASN* 3.0 25.2 - - - +
344D ALA* 4.0 5.2 - - + -
365D LEU 3.0 18.4 + - - +
366D MET 4.3 2.7 - - - +
367D ARG 3.6 0.4 - - - -
368D ASP* 1.3 77.4 - - - +
370D LYS* 1.3 63.1 + - - +
371D ILE 3.0 1.7 + - - -
372D TYR* 3.1 17.5 + - - +
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Residues in contact with LYS 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C THR* 3.0 35.8 + - - +
348C VAL* 3.6 25.8 - - + -
349C GLN* 2.9 24.8 + - - +
356C PHE* 4.2 6.1 - - + -
366C MET* 3.6 18.2 - - + -
215D MET* 3.8 25.8 - - + -
341D ASN* 3.1 14.0 - - - +
366D MET 3.9 5.7 + - - +
367D ARG 4.3 1.6 - - - +
368D ASP 3.2 1.6 + - - -
369D ALA* 1.3 75.7 - - - +
371D ILE* 1.3 60.2 + - - +
372D TYR 3.3 0.2 - - - -
373D GLN* 2.8 32.3 + - - +
374D ILE* 3.5 15.4 - - + +
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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