Contacts of the helix formed by residues 438 - 450 (chain D) in PDB entry 4QG0
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 LEU 438 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392D LYS 5.5 0.4 - - - -
393D ALA* 3.5 39.5 - - + +
396D TYR* 4.1 21.8 - - + -
397D ILE* 4.2 22.0 - - + +
429D GLU 5.4 0.2 - - - +
430D ILE* 5.0 5.8 - - + +
433D SER* 3.6 33.0 - - - +
435D ASP* 3.2 21.2 + - + +
436D PRO 3.0 1.2 - - - -
437D LYS* 1.3 77.8 - - - +
439D LYS* 1.3 66.7 + - - +
440D ASP* 3.3 2.5 - - - -
441D ALA* 3.0 9.9 + - + +
442D ARG* 2.9 22.6 + - - +
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Residues in contact with LYS 439 (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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435D ASP 3.6 2.8 + - - -
436D PRO* 2.9 20.4 + - + +
437D LYS 3.5 0.2 - - - -
438D LEU* 1.3 75.0 - - - +
440D ASP* 1.3 66.0 + - - +
442D ARG* 2.9 28.5 + - - +
443D GLU* 2.7 50.1 + - + +
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Residues in contact with ASP 440 (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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392D LYS* 3.9 30.1 - - + +
437D LYS 5.2 2.4 + - - +
438D LEU 3.3 0.6 - - - -
439D LYS* 1.3 94.3 + - - +
441D ALA* 1.3 64.1 + - - +
443D GLU* 3.0 17.7 + - - +
444D ILE* 3.1 15.8 + - - +
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Residues in contact with ALA 441 (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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389D ALA* 3.4 33.9 - - - +
392D LYS* 4.1 13.4 + - + +
393D ALA* 3.8 17.5 - - + +
430D ILE* 3.8 17.7 - - + -
438D LEU* 3.0 11.6 + - + +
440D ASP* 1.3 77.0 - - - +
442D ARG* 1.3 64.7 + - - +
444D ILE* 3.0 16.2 + - - +
445D LEU* 3.2 9.5 + - - +
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Residues in contact with ARG 442 (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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430D ILE* 3.6 20.6 - - - +
431D LEU* 3.8 16.6 - - - +
433D SER* 3.0 49.3 + - - -
434D THR* 3.6 9.5 + - - +
435D ASP 2.8 27.5 + - - -
436D PRO* 4.8 1.8 - - - +
438D LEU 2.9 10.7 + - - +
439D LYS* 3.1 35.5 - - - +
441D ALA* 1.3 77.2 - - - +
443D GLU* 1.3 65.1 + - - +
445D LEU* 3.0 8.0 + - - +
446D LYS* 2.9 42.1 + - + +
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Residues in contact with GLU 443 (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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439D LYS* 2.7 36.0 + - + +
440D ASP* 3.0 11.4 + - - +
442D ARG* 1.3 75.9 + - - +
444D ILE* 1.3 64.4 + - + +
446D LYS* 3.0 27.3 + - - +
447D GLN* 2.9 25.6 + - - +
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Residues in contact with ILE 444 (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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385D MET* 3.3 42.6 - - + +
388D ASP* 4.2 8.3 - - + -
389D ALA* 4.0 19.3 - - + +
392D LYS* 3.6 39.0 - - + +
440D ASP 3.1 7.5 + - - +
441D ALA 3.0 8.3 + - - +
443D GLU* 1.3 76.2 - - + +
445D LEU* 1.3 65.5 + - + +
447D GLN* 2.9 35.3 + - - +
448D ILE* 3.3 6.9 + - - +
454D PHE* 5.8 6.1 - - + -
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Residues in contact with LEU 445 (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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386D ILE* 4.5 8.5 - - + -
389D ALA* 3.6 22.9 - - + -
390D PHE* 5.6 0.9 - - + -
427D PHE* 3.2 61.6 - - + +
430D ILE* 3.6 24.7 - - + -
431D LEU* 3.7 19.3 - - + +
441D ALA 3.8 9.2 - - - +
442D ARG 3.0 7.9 + - - +
444D ILE* 1.3 77.5 - - + +
446D LYS* 1.3 58.7 + - - +
448D ILE* 2.9 32.3 + - + +
449D GLU* 3.2 13.9 + - - +
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Residues in contact with LYS 446 (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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139A PRO* 6.3 0.8 - - - +
421A LYS* 6.3 1.4 - - - +
431D LEU* 3.6 32.9 + - + +
432D TYR* 6.2 0.4 - - - -
442D ARG* 2.9 39.2 + - + +
443D GLU* 3.0 32.5 + - - +
445D LEU* 1.3 74.9 - - - +
447D GLN* 1.3 65.4 + - - +
449D GLU* 3.0 22.5 + - + +
450D TYR* 3.1 38.0 + - + -
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Residues in contact with GLN 447 (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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385D MET* 3.7 11.1 - - + +
443D GLU* 2.9 14.3 + - - +
444D ILE* 3.1 30.0 - - - +
446D LYS* 1.3 77.7 - - - +
448D ILE* 1.3 58.7 + - - +
450D TYR* 3.5 2.6 + - - -
451D ARG* 3.1 2.9 + - - -
452D ASN* 2.8 67.6 + - + +
453D LEU 5.1 0.6 - - - -
454D PHE* 4.2 23.0 - - - -
555D LYS 5.5 1.8 + - - -
557D VAL* 5.4 6.1 - - - +
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Residues in contact with ILE 448 (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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142A GLN* 5.6 1.2 - - - +
155D TYR* 4.5 24.9 - - + -
382D ILE* 4.4 18.2 - - + +
385D MET* 3.8 31.2 - - + -
386D ILE* 3.8 28.9 - - + -
427D PHE* 4.5 8.7 - - + -
444D ILE 3.3 8.9 + - - +
445D LEU* 2.9 27.6 + - + +
447D GLN* 1.3 77.4 - - - +
449D GLU* 1.3 62.9 + - + +
451D ARG* 3.1 21.0 + - - +
453D LEU* 4.0 13.5 - - + +
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Residues in contact with GLU 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASP* 3.6 20.1 - - - +
138A THR 3.9 1.1 + - - -
139A PRO* 3.4 41.9 - - + +
142A GLN* 3.8 33.3 - - + +
143A ARG* 4.8 1.7 + - - -
146A TYR* 4.5 13.3 + - - +
427D PHE* 5.6 5.6 - - + -
431D LEU* 3.4 35.6 - - + +
445D LEU 3.2 10.8 + - - +
446D LYS* 3.0 15.9 + - - +
448D ILE* 1.3 77.5 - - + +
450D TYR* 1.3 62.2 - - + +
451D ARG* 3.2 0.9 + - - -
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Residues in contact with TYR 450 (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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137A ASP* 3.8 22.6 - - - +
138A THR* 5.7 0.2 - - + -
139A PRO* 3.7 27.3 - - + +
247A SER 5.7 0.7 + - - -
248A ASN* 3.6 23.9 + - - -
446D LYS* 3.1 44.0 + - + +
447D GLN* 4.2 2.0 - - - +
449D GLU* 1.3 77.2 - - + +
451D ARG* 1.3 70.0 + - - +
452D ASN* 3.3 26.1 + - - +
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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