Contacts of the helix formed by residues 431 - 442 (chain F) in PDB entry 4LQL
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 GLY 431 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428F PRO* 3.3 6.9 + - - -
429F GLU 2.4 22.3 + - - -
430F ILE* 1.3 68.5 - - - +
432F LEU* 1.3 56.2 + - - -
433F ALA 3.2 2.5 - - - -
434F GLU* 2.5 32.9 + - - -
435F GLY 2.9 11.3 + - - -
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Residues in contact with LEU 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ARG* 5.3 3.6 - - - +
335F LEU* 5.0 9.4 - - + -
336F ASP 4.2 10.1 - - - +
337F LEU* 6.4 0.4 - - + -
342F GLU* 3.6 42.8 - - + +
343F ALA* 4.6 7.9 - - - +
344F ILE* 4.7 21.3 - - + -
427F THR* 5.5 2.2 - - - -
428F PRO* 4.0 20.5 + - + +
431F GLY* 1.3 69.9 - - - +
433F ALA* 1.3 65.8 + - + +
435F GLY 4.8 0.2 - - - +
436F ALA* 3.4 27.8 + - + +
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Residues in contact with ALA 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TYR* 4.7 24.5 - - + +
149D GLY* 6.2 0.2 - - - -
431F GLY 2.9 2.0 + - - -
432F LEU* 1.3 82.3 - - + +
434F GLU* 1.3 62.4 + - + +
436F ALA 4.1 0.9 - - - -
437F LYS* 3.0 33.1 + - + +
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Residues in contact with GLU 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430F ILE* 3.2 30.5 - - + +
431F GLY* 2.5 14.5 + - - +
433F ALA* 1.3 74.1 - - + +
435F GLY* 1.3 57.5 + - - +
437F LYS* 2.7 31.4 + - - +
438F GLN* 3.0 9.8 + - - +
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Residues in contact with GLY 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F TYR* 4.7 9.3 - - - -
428F PRO* 5.1 5.2 - - - -
429F GLU 4.8 2.0 - - - -
430F ILE* 3.7 17.1 - - - +
431F GLY 2.9 15.9 + - - -
432F LEU 4.5 0.4 - - - -
434F GLU* 1.3 72.9 - - - +
436F ALA* 1.3 55.0 + - - +
438F GLN* 3.5 2.9 + - - +
439F TRP* 2.9 29.5 + - - +
473F ILE* 4.3 14.0 - - - +
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Residues in contact with ALA 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ARG* 3.2 33.7 - - - +
148D TYR* 4.6 10.5 - - + -
428F PRO* 5.8 1.2 - - - +
432F LEU* 3.4 22.4 + - + +
433F ALA* 4.1 2.9 - - - +
434F GLU 3.3 0.4 - - - -
435F GLY* 1.3 72.4 - - - +
437F LYS* 1.3 58.1 + - - +
439F TRP* 3.8 10.5 - - + -
440F MET* 3.0 30.7 - - + +
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Residues in contact with LYS 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D SER* 5.2 13.9 - - - +
148D TYR* 4.5 17.3 - - + +
433F ALA* 3.0 19.6 + - + +
434F GLU* 2.7 17.2 + - - +
436F ALA* 1.3 77.6 - - - +
438F GLN* 1.3 59.8 + - - +
439F TRP 2.9 4.1 + - - -
440F MET* 4.7 1.3 - - - -
441F LYS* 3.0 34.6 + - + +
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Residues in contact with GLN 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434F GLU 3.0 9.2 + - - +
435F GLY 4.1 5.2 - - - +
437F LYS* 1.3 75.3 - - - +
439F TRP* 1.3 55.9 + - - +
441F LYS* 4.6 3.8 - - - -
442F TYR* 3.3 30.6 + - - +
473F ILE* 4.1 28.7 - - + +
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Residues in contact with TRP 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ARG* 3.5 22.5 - - - +
390F ASP* 3.9 23.1 - - - -
392F THR* 3.8 26.9 - - - -
403F ILE* 3.9 17.9 - - + -
405F TYR* 4.2 20.2 - - + -
435F GLY 2.9 19.0 + - - +
436F ALA* 3.8 6.5 - - - -
437F LYS 2.9 2.2 - - - -
438F GLN* 1.3 75.8 - - - +
440F MET* 1.3 70.3 + - - +
441F LYS 2.9 2.9 + - - -
442F TYR 3.1 11.2 - - - +
443F GLY 2.8 19.6 - - - +
444F GLY* 3.1 29.6 - - - -
445F GLY 3.4 18.8 + - - +
447F HIS 5.1 0.4 - - - -
448F THR* 3.7 27.8 - - - -
473F ILE* 4.4 11.7 - - + -
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Residues in contact with MET 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D HIS* 5.9 1.6 - - + -
104D ALA* 5.4 8.1 - - + -
130D ASP* 4.8 7.2 - - + +
131D ARG* 4.1 31.4 - - + +
134D ALA* 3.1 43.4 - - + +
146D SER* 4.9 14.1 - - - +
148D TYR* 5.5 1.3 - - + -
436F ALA* 3.0 22.3 + - + +
437F LYS* 4.3 2.9 - - - +
439F TRP* 1.3 81.7 - - - +
441F LYS* 1.3 62.7 + - + +
443F GLY 3.3 8.1 - - - +
444F GLY 5.0 1.6 - - - -
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Residues in contact with LYS 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D SER* 3.4 19.3 - - - -
146D SER* 5.4 12.1 - - - -
437F LYS* 3.0 24.5 + - + +
438F GLN* 4.3 3.6 - - - +
439F TRP 2.9 1.2 + - - -
440F MET* 1.3 75.4 - - + +
442F TYR* 1.3 56.9 + - - +
443F GLY 2.7 22.9 + - - +
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Residues in contact with TYR 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403F ILE* 3.8 14.8 - - - +
438F GLN* 3.3 16.8 + - + +
439F TRP* 3.1 12.5 - - - +
441F LYS* 1.3 75.2 - - + +
443F GLY* 1.3 57.0 + - - +
471F ILE* 5.0 14.4 - - + +
473F ILE* 5.5 0.6 - - + +
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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