Contacts of the helix formed by residues 400 - 418 (chain A) in PDB entry 2PU1
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 ARG 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A SER* 2.9 32.1 + - - -
15A ARG* 5.0 3.8 - - - +
205A VAL* 4.2 16.3 + - + +
206A GLY 2.8 19.0 + - - -
207A ASP* 3.2 22.1 + - - +
209A GLY* 3.4 28.9 - - - +
399A CYS* 1.3 85.7 - - - +
401A GLY* 1.3 54.8 + - - +
402A GLU* 2.8 34.0 + - - +
403A ARG* 2.8 24.9 + - + -
404A THR* 2.9 16.2 + - - +
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Residues in contact with GLY 401 (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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377A GLU* 5.1 2.2 - - - +
400A ARG* 1.3 71.7 - - - +
402A GLU* 1.3 58.3 + - - +
403A ARG 3.1 0.7 - - - -
404A THR* 3.3 12.5 + - - -
405A ALA* 2.9 32.2 + - - +
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Residues in contact with GLU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 3.2 28.0 - - - -
207A ASP 3.3 0.2 - - - +
375A GLU* 3.5 14.3 - - + +
376A THR* 3.4 28.7 - - - +
377A GLU* 4.6 1.3 - - - +
395A THR* 4.7 0.3 + - - -
400A ARG* 2.8 42.0 + - - +
401A GLY* 1.3 72.7 + - - -
403A ARG* 1.3 91.2 + - - +
405A ALA* 4.8 0.9 - - - -
406A LYS* 2.8 32.8 + - - +
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Residues in contact with ARG 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 3.4 10.9 + - - -
207A ASP 3.0 16.5 + - - -
208A GLU* 3.7 21.1 - - - +
371A HIS* 2.9 25.5 + - - -
372A ARG 2.9 17.0 + - - -
373A SER 2.7 25.4 + - - -
375A GLU* 3.3 8.8 - - - +
395A THR* 3.2 24.7 - - - +
396A GLY* 3.8 7.0 - - - -
397A ALA 3.4 16.8 - - - +
399A CYS 3.4 17.0 - - - +
400A ARG* 2.8 8.0 + - + +
402A GLU* 1.3 105.3 + - - +
404A THR* 1.3 65.0 + - - +
405A ALA 3.1 1.3 - - - -
406A LYS* 3.1 17.7 + - - +
407A LEU* 3.3 15.2 + - + +
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Residues in contact with THR 404 (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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398A PRO* 3.8 11.9 - - + +
399A CYS* 3.7 28.5 - - - +
400A ARG 2.9 8.5 + - - +
401A GLY* 3.3 21.0 - - - -
403A ARG* 1.3 73.8 - - - +
405A ALA* 1.3 56.4 + - - +
407A LEU* 3.7 9.8 - - + -
408A ASN* 2.8 47.6 + - - -
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Residues in contact with ALA 405 (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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377A GLU* 4.1 17.3 - - + +
379A THR* 3.4 27.5 - - + +
401A GLY 2.9 22.0 + - - +
402A GLU 4.8 0.4 - - - -
403A ARG 3.1 0.2 - - - -
404A THR* 1.3 78.4 + - - +
406A LYS* 1.3 59.9 + - + +
408A ASN* 3.8 7.9 - - - +
409A GLN* 3.0 22.2 + - - +
412A ARG* 4.5 2.5 + - - +
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Residues in contact with LYS 406 (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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375A GLU* 2.8 30.1 + - - +
376A THR 2.7 29.9 + - - -
378A ASP* 2.8 22.7 + - - +
379A THR* 4.3 9.4 - - - -
381A ILE* 3.6 26.5 - - + -
382A ALA* 3.6 11.7 - - + +
393A ILE* 5.2 2.2 - - + -
395A THR* 3.2 31.9 - - + +
402A GLU 2.8 21.8 + - - +
403A ARG 3.1 4.9 + - - +
405A ALA* 1.3 75.3 - - + +
407A LEU* 1.3 65.5 + - - +
409A GLN 3.2 1.2 + - - -
410A LEU* 3.0 27.3 + - - +
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Residues in contact with LEU 407 (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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146A PRO* 4.2 7.9 - - + -
148A PHE* 3.9 27.1 - - + -
176A PHE* 3.4 23.0 - - + -
180A LEU* 3.7 32.8 - - + -
395A THR* 3.6 23.3 - - + -
396A GLY 5.0 0.7 - - - +
397A ALA 4.2 5.6 - - - +
398A PRO* 3.9 19.5 - - + -
403A ARG* 3.6 13.5 - - + +
404A THR* 3.2 15.4 + - + +
406A LYS* 1.3 75.0 - - - +
408A ASN* 1.3 65.1 + - - +
410A LEU* 3.3 8.9 + - + +
411A LEU* 3.0 19.6 + - - +
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Residues in contact with ASN 408 (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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180A LEU* 4.8 4.2 - - - +
404A THR* 2.8 32.1 + - - +
405A ALA* 3.8 6.2 - - - +
407A LEU* 1.3 79.4 - - - +
409A GLN* 1.3 61.8 + - - +
411A LEU* 3.1 26.6 + - + +
412A ARG* 3.1 45.7 + - - +
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Residues in contact with GLN 409 (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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379A THR* 3.9 19.5 + - - +
382A ALA* 3.5 20.0 - - + -
383A ASP* 2.8 28.0 + - - +
405A ALA 3.0 19.5 + - - +
406A LYS 3.2 4.9 + - - +
408A ASN* 1.3 77.2 - - - +
410A LEU* 1.3 55.6 - - - +
412A ARG* 3.0 34.9 + - - +
413A ILE* 2.9 30.0 + - + +
700A EDO 3.0 37.5 + - - -
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Residues in contact with LEU 410 (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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143A LEU* 3.5 7.0 - - + +
144A PRO* 4.0 21.3 - - + -
176A PHE* 3.4 37.0 - - + -
382A ALA* 3.5 31.6 - - + +
385A VAL* 4.1 1.3 - - + -
386A VAL* 3.7 19.7 - - + -
393A ILE* 4.1 21.5 - - + -
406A LYS 3.0 17.7 + - - +
407A LEU* 3.4 14.6 - - + +
408A ASN 3.2 0.2 - - - -
409A GLN* 1.3 72.2 - - - +
411A LEU* 1.3 59.0 + - - +
413A ILE* 3.4 2.6 + - + +
414A GLU* 2.9 30.8 + - - +
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Residues in contact with LEU 411 (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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176A PHE* 3.9 14.7 - - + -
177A SER* 3.6 30.3 - - - +
180A LEU* 3.8 19.3 - - + -
407A LEU 3.0 14.6 + - - +
408A ASN* 3.1 30.5 + - + +
410A LEU* 1.3 72.9 - - - +
412A ARG* 1.3 58.7 + - + +
414A GLU* 3.4 11.9 + - - +
415A GLU* 3.0 29.5 + - - +
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Residues in contact with ARG 412 (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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379A THR* 5.4 2.8 - - - +
405A ALA* 4.5 3.2 + - - +
408A ASN* 3.1 30.4 + - - +
409A GLN* 3.0 45.6 + - - +
411A LEU* 1.3 73.4 - - + +
413A ILE* 1.3 67.0 + - - +
415A GLU* 3.3 12.1 + - - +
416A GLU* 3.1 25.9 + - - +
700A EDO 4.0 22.7 - - - -
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Residues in contact with ILE 413 (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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129A TYR* 3.7 31.6 - - + -
143A LEU* 4.7 0.9 - - + -
382A ALA* 3.8 9.2 - - + +
383A ASP* 3.8 43.7 - - - +
386A VAL* 3.9 20.4 - - + -
409A GLN* 2.9 25.2 + - + +
410A LEU* 3.8 5.6 - - + +
412A ARG* 1.3 73.7 - - - +
414A GLU* 1.3 65.9 + - - +
416A GLU* 3.0 6.5 + - - +
417A LEU* 3.0 40.4 + - + +
700A EDO 3.9 12.6 - - - -
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Residues in contact with GLU 414 (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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143A LEU* 3.9 27.3 - - + +
175A SER* 3.5 11.8 - - - -
176A PHE* 3.1 15.2 + - + +
177A SER* 2.5 48.9 + - - -
410A LEU 2.9 18.3 + - - +
411A LEU* 3.5 13.6 - - - +
413A ILE* 1.3 76.1 - - - +
415A GLU* 1.3 62.7 + - - +
417A LEU* 3.3 2.5 + - - +
418A GLY* 3.0 26.5 + - - +
421A ALA* 5.2 1.3 - - + +
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Residues in contact with GLU 415 (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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411A LEU 3.0 13.8 + - - +
412A ARG* 3.5 12.9 - - - +
413A ILE 3.2 0.2 - - - -
414A GLU* 1.3 78.5 - - - +
416A GLU* 1.3 65.0 + - - +
417A LEU 3.4 0.2 + - - -
418A GLY* 3.4 10.7 + - - -
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Residues in contact with GLU 416 (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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127A PRO* 3.7 9.4 - - - +
129A TYR* 2.7 32.7 + - - +
412A ARG 3.1 12.9 + - - +
413A ILE 3.0 9.0 + - - +
415A GLU* 1.3 81.2 - - + +
417A LEU* 1.3 63.3 - - - +
418A GLY* 4.7 0.5 - - - -
700A EDO 3.2 36.2 + - - -
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Residues in contact with LEU 417 (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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129A TYR* 3.7 23.8 - - + +
130A ARG* 3.5 28.0 - - - +
141A LEU* 3.9 15.9 - - + -
143A LEU* 3.9 18.6 - - + -
386A VAL* 4.2 12.6 - - + -
413A ILE* 3.0 32.4 + - + +
414A GLU 4.0 2.5 - - - +
416A GLU* 1.3 77.6 - - - +
418A GLY* 1.3 63.9 + - - +
420A HIS* 4.8 1.4 + - - +
421A ALA* 3.6 23.5 + - + +
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Residues in contact with GLY 418 (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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414A GLU* 3.0 15.6 + - - +
415A GLU* 3.4 8.3 + - - -
416A GLU 3.4 2.0 - - - -
417A LEU* 1.3 77.0 - - - +
419A ALA* 1.3 65.9 + - - -
420A HIS 3.1 4.3 + - - -
421A ALA* 3.2 17.0 + - - +
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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