Contacts of the helix formed by residues 370 - 383 (chain D) in PDB entry 5UQ9
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 370 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228D LEU 4.2 3.1 - - - -
229D ASP 3.3 17.5 - - - -
230D SER* 3.6 14.4 - - - +
331D LYS* 3.8 6.4 + - - -
363D ARG* 3.3 28.7 + - - +
368D ILE 3.4 2.8 + - - -
369D ARG* 1.3 77.2 - - - +
371D VAL* 1.3 63.7 + - - +
372D PHE* 3.4 15.1 + - - +
373D LEU* 3.3 28.1 + - - +
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Residues in contact with VAL 371 (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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226D THR 5.0 0.7 - - - +
227D GLU* 4.2 11.7 - - - +
228D LEU 3.6 16.2 - - - +
229D ASP* 3.3 32.4 + - + +
363D ARG* 3.3 24.1 + - - +
370D SER* 1.3 72.4 - - - +
372D PHE* 1.3 66.2 + - - +
373D LEU 3.2 0.2 - - - -
374D GLY* 3.1 11.7 + - - -
375D LYS* 3.4 25.4 + - + +
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Residues in contact with PHE 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D GLU 4.5 5.6 - - - +
228D LEU* 4.4 8.7 - - - +
328D TYR* 3.8 25.1 - + + -
331D LYS* 3.0 28.5 - - + +
332D ILE* 3.7 35.9 - - + -
335D TYR* 3.4 30.1 - + + -
370D SER* 3.1 10.6 - - - +
371D VAL* 1.3 82.3 - - - +
373D LEU* 1.3 65.5 + - + +
375D LYS* 3.2 17.0 + - + +
376D ILE* 3.2 32.2 + - + +
389D LEU* 5.1 0.9 - - + -
395D PHE* 3.4 26.2 - + - -
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Residues in contact with LEU 373 (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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335D TYR* 3.6 36.1 - - + +
339D PHE* 5.2 0.4 - - + -
359D ALA* 3.7 43.7 - - + +
362D TRP* 4.1 20.0 - - + -
363D ARG* 3.9 9.2 - - + -
368D ILE* 3.4 20.6 - - + +
370D SER* 3.3 31.1 + - - +
371D VAL 3.2 0.6 - - - -
372D PHE* 1.3 80.3 - - + +
374D GLY* 1.3 57.0 + - - +
376D ILE* 3.2 14.4 + - + +
377D LYS* 2.9 26.0 + - - +
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Residues in contact with GLY 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D ARG* 3.7 21.5 - - - +
371D VAL 3.1 11.9 + - - -
373D LEU* 1.3 78.4 - - - +
375D LYS* 1.3 57.9 + - - +
377D LYS* 3.0 9.5 + - - +
378D ASP* 3.0 36.0 + - - +
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Residues in contact with LYS 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D TYR* 5.3 2.2 - - - +
371D VAL* 3.4 24.0 + - + +
372D PHE* 3.2 12.2 + - + +
374D GLY* 1.3 76.3 - - - +
376D ILE* 1.3 57.2 + - - +
378D ASP* 3.4 18.3 + - - +
379D ALA 3.1 20.3 + - - -
382D ARG* 4.4 5.0 + - - +
394D PHE* 3.8 40.2 - - + -
395D PHE* 3.5 23.9 - - + -
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Residues in contact with ILE 376 (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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335D TYR* 3.7 28.7 - - + -
339D PHE* 3.8 26.9 - - + -
359D ALA* 3.9 7.6 - - + -
372D PHE* 3.2 38.0 + - + +
373D LEU* 3.2 15.4 + - + +
374D GLY 3.2 0.6 - - - -
375D LYS* 1.3 74.4 - - - +
377D LYS* 1.3 64.3 + - - +
379D ALA* 3.1 10.7 + - - +
380D PHE* 3.2 26.3 + - + -
389D LEU* 4.0 12.3 - - + -
395D PHE* 3.6 21.3 - - + -
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Residues in contact with LYS 377 (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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168D GLU* 3.6 15.0 + - - -
356D GLY* 3.2 32.3 + - - +
357D GLY* 5.0 1.6 - - - +
359D ALA* 4.1 3.8 - - + +
360D LEU* 3.6 38.7 - - + +
363D ARG* 6.3 0.4 - - - -
373D LEU 2.9 12.5 + - - +
374D GLY* 3.0 13.0 + - - +
376D ILE* 1.3 76.9 - - - +
378D ASP* 1.3 65.9 + - - +
380D PHE* 3.3 4.7 + - - +
381D ASP* 3.1 63.6 + - - +
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Residues in contact with ASP 378 (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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374D GLY* 3.0 18.6 + - - +
375D LYS* 3.4 24.2 + - - +
377D LYS* 1.3 80.3 - - - +
379D ALA* 1.3 61.8 + - - +
381D ASP* 3.2 12.9 + - - +
382D ARG* 3.2 46.9 + - + +
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Residues in contact with ALA 379 (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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375D LYS 3.1 5.6 + - - +
376D ILE 3.1 10.2 + - - +
378D ASP* 1.3 77.8 - - - +
380D PHE* 1.3 59.4 + - - +
382D ARG* 3.1 14.2 + - - +
383D ASN* 3.7 13.3 + - - +
386D LEU* 3.8 13.8 - - + +
389D LEU* 3.8 14.6 - - + -
392D ASP* 3.6 17.5 - - + +
395D PHE* 3.5 30.5 - - + -
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Residues in contact with PHE 380 (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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339D PHE* 3.5 46.0 - + + -
343D ARG* 4.5 4.5 - - - -
355D TYR* 3.5 30.7 - + + -
356D GLY* 3.7 23.8 - - - +
376D ILE* 3.2 33.4 + - + -
377D LYS 3.3 1.1 + - - +
378D ASP 3.2 0.4 - - - -
379D ALA* 1.3 76.5 - - - +
381D ASP* 1.3 62.4 + - - +
382D ARG 3.3 0.4 - - - -
383D ASN 3.7 12.6 - - - -
384D PRO* 3.0 42.6 - - + +
386D LEU* 4.3 24.9 - - + -
388D ASN 6.4 0.2 - - - -
389D LEU* 4.3 15.9 - - + -
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Residues in contact with ASP 381 (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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356D GLY* 5.2 3.1 - - - -
377D LYS* 3.1 49.6 + - - +
378D ASP* 3.2 13.4 + - - +
380D PHE* 1.3 79.6 - - - +
382D ARG* 1.3 63.8 + - + +
383D ASN 3.4 0.5 + - - -
384D PRO* 4.0 8.3 - - - +
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Residues in contact with ARG 382 (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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375D LYS* 4.4 5.9 + - - +
378D ASP* 3.2 36.9 + - + +
379D ALA* 3.1 16.1 - - - +
380D PHE 3.3 0.2 - - - -
381D ASP* 1.3 76.7 - - + +
383D ASN* 1.3 62.4 + - + +
384D PRO* 4.1 1.8 - - - +
392D ASP* 2.3 47.1 + - - +
393D ASP* 6.0 1.5 - - - +
394D PHE* 4.3 15.2 - - - +
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Residues in contact with ASN 383 (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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379D ALA 3.7 5.9 + - - +
380D PHE* 3.1 11.5 + - - +
381D ASP 3.2 0.4 - - - -
382D ARG* 1.3 83.4 - - + +
384D PRO* 1.3 67.4 - - - +
385D GLU* 3.1 26.3 + - - +
386D LEU* 3.2 47.3 + - + +
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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