Contacts of the helix formed by residues 421 - 435 (chain A) in PDB entry 1G1U
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 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A GLU 2.7 37.8 + - - -
353A LEU* 4.3 9.2 - - + +
356A LYS* 3.8 26.3 - - + +
357A MET* 5.6 4.3 - - + -
360A MET* 5.3 5.6 - - - -
362A MET* 4.6 20.2 - - + -
370A LEU* 5.2 3.8 - - + -
417A LYS 3.5 12.3 + - - +
418A LEU* 3.2 11.1 + - - +
419A LEU 3.2 1.0 - - - -
420A LEU* 1.3 97.3 + - - +
422A LEU* 1.3 65.6 + - + +
423A PRO 3.3 1.1 - - - -
424A ALA* 3.1 17.9 + - - +
425A LEU* 3.1 20.8 + - - +
378B PRO* 4.8 7.9 - - - +
379B ASP* 3.1 37.1 + - - -
390B GLU* 5.5 2.6 + - - -
393B ARG* 4.3 12.3 - - - +
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Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 4.9 2.1 - - - +
370A LEU* 4.2 30.7 - - + -
373A ILE* 4.1 17.0 - - + -
374A VAL* 4.3 14.6 - - + -
418A LEU 4.6 1.1 - - - +
419A LEU* 3.3 22.6 + - + +
421A ARG* 1.3 75.7 - - + +
423A PRO* 1.3 63.4 - - + +
425A LEU* 3.2 25.2 + - + +
426A ARG* 2.9 27.5 + - - +
420B LEU* 3.8 27.6 - - + -
423B PRO* 3.7 16.5 - - + +
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Residues in contact with PRO 423 (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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419A LEU 3.8 4.0 - - - +
420A LEU* 3.6 22.0 - - + +
421A ARG 3.5 3.6 - - - -
422A LEU* 1.3 94.3 - - + +
424A ALA* 1.3 59.7 - - - +
426A ARG* 3.0 3.7 + - + +
427A SER* 2.9 23.6 + - - -
393B ARG* 6.2 0.4 - - - +
422B LEU* 3.8 29.4 - - + +
423B PRO* 4.0 14.8 - - + -
426B ARG* 3.3 35.7 + - + +
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Residues in contact with ALA 424 (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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352A GLU* 3.7 19.5 - - + +
353A LEU* 3.9 11.9 - - + -
420A LEU 5.0 0.8 + - - +
421A ARG* 3.1 34.3 + - - +
423A PRO* 1.3 78.7 - - - +
425A LEU* 1.3 55.2 + - - +
427A SER* 3.2 3.1 + - - -
428A ILE* 2.8 41.0 + - - +
379B ASP* 4.2 5.2 - - - +
426B ARG* 3.6 10.5 - - - +
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 3.6 51.4 - - + +
308A LEU* 6.4 0.2 - - + -
310A ILE* 3.9 24.5 - - + -
311A ALA* 4.0 17.9 - - + +
353A LEU* 4.0 17.0 - - + +
357A MET* 6.3 0.2 - - + -
370A LEU* 6.2 1.1 - - + -
374A VAL* 3.9 20.0 - - + -
421A ARG 3.1 9.1 + - - +
422A LEU* 3.4 21.3 - - + +
423A PRO 3.2 0.2 - - - -
424A ALA* 1.3 79.9 - - - +
426A ARG* 1.3 61.5 + - - +
428A ILE* 4.0 2.6 - - - +
429A GLY* 3.0 18.2 + - - -
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Residues in contact with ARG 426 (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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307A GLU* 2.7 34.4 + - - +
377A ASN* 3.9 25.2 + - - +
379A ASP* 5.3 5.7 + - - +
393A ARG* 5.9 4.2 - - - +
422A LEU 2.9 13.0 + - - +
423A PRO* 3.0 11.2 + - + +
425A LEU* 1.3 78.8 - - - +
427A SER* 1.3 63.3 + - - +
429A GLY* 3.2 1.4 + - - -
430A LEU* 3.1 27.7 + - - +
352B GLU* 4.9 3.2 + - - -
423B PRO* 3.4 41.6 + - + +
424B ALA* 3.8 6.7 - - - +
426B ARG* 4.4 0.2 - - + -
427B SER* 3.0 42.1 + - - +
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Residues in contact with SER 427 (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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348A ARG* 2.7 33.2 + - - -
423A PRO 2.9 6.5 + - - -
424A ALA 3.2 4.5 + - - -
426A ARG* 1.3 72.3 - - - +
428A ILE* 1.3 64.8 + - - +
430A LEU* 3.4 3.1 + - - +
431A LYS* 3.0 27.7 + - - +
426B ARG* 3.1 37.9 + - - -
430B LEU* 3.6 20.1 - - - +
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Residues in contact with ILE 428 (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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310A ILE* 4.2 14.1 - - + -
345A ILE* 3.8 12.6 - - + -
348A ARG* 3.5 55.9 - - + +
349A VAL* 3.7 21.3 - - + +
352A GLU* 4.2 10.5 - - + -
353A LEU* 3.7 22.4 - - + -
424A ALA 2.8 23.8 + - - +
425A LEU* 4.0 3.8 - - - +
427A SER* 1.3 71.9 - - - +
429A GLY* 1.3 59.1 + - - +
431A LYS* 3.2 3.3 + - - +
432A CYS* 2.8 36.6 + - - +
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Residues in contact with GLY 429 (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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306A ASN* 2.8 34.3 + - - -
307A GLU* 4.7 4.9 - - - -
310A ILE* 3.7 10.5 - - - -
425A LEU 3.0 15.9 + - - -
426A ARG 3.6 3.8 - - - -
428A ILE* 1.3 78.7 - - - +
430A LEU* 1.3 63.2 + - - +
432A CYS* 3.2 1.0 + - - +
433A LEU* 3.1 17.0 + - - +
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Residues in contact with LEU 430 (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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426A ARG* 3.1 22.1 + - + +
427A SER* 3.8 6.7 - - - +
429A GLY* 1.3 75.3 - - - +
431A LYS* 1.3 58.7 + - - +
433A LEU* 3.2 17.1 + - + +
434A GLU* 2.9 43.0 + - + +
427B SER* 3.6 36.6 - - - +
430B LEU* 4.4 15.3 - - + -
431B LYS* 4.2 26.5 - - + +
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Residues in contact with LYS 431 (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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345A ILE* 3.6 19.4 - - + +
348A ARG* 3.9 15.5 - - - +
427A SER 3.0 19.3 + - - +
428A ILE 3.6 3.8 - - - +
430A LEU* 1.3 78.0 - - - +
432A CYS* 1.3 62.2 + - - +
434A GLU* 3.0 32.4 + - - +
435A HIS* 3.0 50.9 + - + +
430B LEU* 4.5 29.5 - - + +
434B GLU* 5.4 1.0 + - - +
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Residues in contact with CYS 432 (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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306A ASN* 4.6 6.5 - - - +
310A ILE* 4.1 17.0 - - + -
313A PHE* 5.9 0.2 - - - -
345A ILE* 3.6 18.2 - - - -
349A VAL* 5.0 2.9 - - - -
428A ILE* 2.8 31.6 + - - +
429A GLY 3.7 4.9 - - - +
431A LYS* 1.3 73.5 - - - +
433A LEU* 1.3 60.8 + - - +
436A LEU* 3.4 1.9 + - - -
437A PHE* 2.9 68.6 + - + +
438A PHE* 4.9 6.0 + - + -
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Residues in contact with LEU 433 (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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305A TRP* 4.3 26.7 - - + +
306A ASN* 3.8 25.4 - - + +
429A GLY 3.1 13.1 + - - +
430A LEU* 3.2 19.7 + - + +
432A CYS* 1.3 76.3 - - - +
434A GLU* 1.3 67.5 + - + +
436A LEU* 3.3 19.5 + - - +
438A PHE* 6.2 1.6 - - + -
434C GLU 5.6 0.9 - - - +
436C LEU* 5.1 25.6 - - + +
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Residues in contact with GLU 434 (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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430A LEU* 2.9 23.2 + - - +
431A LYS* 3.0 42.3 + - - +
433A LEU* 1.3 81.0 - - + +
435A HIS* 1.3 74.8 + - + +
436A LEU* 3.4 14.0 - - - +
430B LEU* 5.6 2.6 - - - +
431B LYS* 4.0 18.9 + - - +
434B GLU* 4.1 14.8 - - - +
434C GLU* 5.4 13.1 - - - +
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Residues in contact with HIS 435 (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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341A GLY 6.1 0.2 - - - +
342A VAL* 3.7 13.0 - - + +
345A ILE* 5.5 9.9 - - + -
431A LYS* 3.0 49.7 + - + +
432A CYS* 5.4 0.2 - - - -
434A GLU* 1.3 91.6 + - + +
436A LEU* 1.3 75.1 + - - +
437A PHE* 2.8 6.8 + - - +
440A LYS* 3.5 19.7 - - + +
435D HIS* 6.5 0.7 - + - -
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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