Contacts of the helix formed by residues 455 - 467 (chain A) 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 SER 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A LYS 5.6 0.3 - - - -
388A GLY* 4.3 15.0 - - - -
389A TYR* 4.4 14.6 - - - -
452A LEU 5.0 0.7 + - - -
453A ALA 3.9 4.0 + - - -
454A LEU* 1.3 90.5 + - - +
456A GLU* 1.3 53.8 + - - +
457A GLU* 2.5 20.3 + - - +
458A GLN* 2.6 23.5 + - - +
459A LEU* 4.5 4.9 - - - -
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Residues in contact with GLU 456 (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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389A TYR* 4.4 11.1 - - + +
404A GLY 5.4 1.1 - - - +
406A PRO* 5.3 13.9 - - + -
455A SER* 1.3 71.8 - - - +
457A GLU* 1.3 64.9 + - - +
458A GLN 3.2 0.2 - - - -
459A LEU* 3.3 16.2 + - - +
460A GLU* 3.3 22.7 + - + +
472A ASN* 4.2 28.0 - - + -
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Residues in contact with GLU 457 (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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159A GLN* 6.1 6.1 - - + -
162A ASP* 4.9 11.4 - - - -
455A SER 2.5 8.0 + - - +
456A GLU* 1.3 77.3 - - - +
458A GLN* 1.3 63.8 + - + +
459A LEU 3.3 0.5 + - - -
460A GLU* 3.6 10.0 + - - +
461A GLN* 3.7 22.3 - - - +
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Residues in contact with GLN 458 (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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162A ASP* 3.5 30.7 - - + +
166A VAL* 2.9 31.8 - - + +
454A LEU* 3.6 38.1 - - + -
455A SER 2.6 22.1 + - - +
457A GLU* 1.3 79.0 - - + +
459A LEU* 1.3 59.2 + - - +
460A GLU 3.4 0.2 - - - -
461A GLN* 3.8 4.8 + - - +
462A LEU* 3.6 8.1 + - - +
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Residues in contact with LEU 459 (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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318A LEU* 5.7 8.5 - - + -
389A TYR* 5.0 13.5 - - + -
391A ILE* 5.5 10.3 - - + -
404A GLY* 6.3 3.1 - - - -
454A LEU* 5.2 15.3 - - + -
455A SER 3.7 7.4 + - - +
456A GLU* 3.3 13.6 + - + +
457A GLU 3.2 0.8 - - - -
458A GLN* 1.3 77.8 - - - +
460A GLU* 1.3 65.9 + - - +
461A GLN 3.3 0.4 - - - -
462A LEU* 3.8 6.3 - - + +
463A ALA* 3.2 25.6 + - - +
470A PHE* 5.2 8.5 - - + -
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Residues in contact with GLU 460 (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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456A GLU* 3.3 25.6 + - + +
457A GLU* 3.8 5.8 - - - +
458A GLN 3.4 0.2 - - - -
459A LEU* 1.3 78.2 - - - +
461A GLN* 1.3 54.1 + - + +
463A ALA* 3.8 3.6 - - - +
464A ARG* 2.7 46.3 + - + +
470A PHE* 5.4 10.9 - - + +
472A ASN* 5.8 6.7 - - + -
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Residues in contact with GLN 461 (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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101A LEU* 5.6 0.8 - - - +
145A ALA* 4.1 18.2 - - + +
146A SER 4.8 11.7 + - - +
147A VAL* 5.9 3.0 - - - +
162A ASP* 5.2 8.8 - - - -
163A TRP* 3.8 38.9 - - + +
166A VAL* 4.6 11.3 - - + +
457A GLU* 3.7 20.9 + - - +
458A GLN 3.8 8.0 + - - +
459A LEU 3.3 0.2 - - - -
460A GLU* 1.3 77.9 - - + +
462A LEU* 1.3 56.7 + - - +
464A ARG* 3.8 8.9 - - - +
465A LEU* 3.6 21.3 + - - +
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Residues in contact with LEU 462 (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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166A VAL* 4.1 16.2 - - + +
169A ALA* 3.9 27.4 - - + -
170A TYR 5.5 0.9 - - - +
318A LEU* 6.3 2.9 - - + -
321A ALA* 6.2 1.3 - - + -
458A GLN 3.6 11.0 + - - +
459A LEU* 3.3 10.6 + - + +
460A GLU 3.2 0.6 - - - -
461A GLN* 1.3 75.4 - - - +
463A ALA* 1.3 68.1 + - - +
464A ARG 3.1 0.7 - - - -
465A LEU* 3.0 17.7 + - + +
466A PHE* 3.6 13.2 + - + -
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Residues in contact with ALA 463 (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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402A PHE* 5.2 4.5 - - + -
459A LEU 3.2 14.4 + - - +
460A GLU 4.0 2.0 - - - +
462A LEU* 1.3 77.0 - - - +
464A ARG* 1.3 58.3 + - + +
465A LEU 2.8 0.9 + - - -
466A PHE* 3.1 5.5 + - - +
467A LYS* 2.7 29.3 + - - -
468A VAL* 3.5 28.5 + - + -
469A ASP 5.0 0.7 - - - +
470A PHE* 4.0 25.8 - - + +
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Residues in contact with ARG 464 (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 PRO* 3.9 23.5 - - - +
460A GLU* 2.7 36.4 + - + +
461A GLN* 4.0 8.1 - - - +
462A LEU 3.1 0.6 - - - -
463A ALA* 1.3 75.1 - - + +
465A LEU* 1.3 59.8 + - - +
467A LYS* 3.3 21.2 + - + +
469A ASP 6.1 0.2 - - - +
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Residues in contact with LEU 465 (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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99A PRO* 4.3 22.2 - - + -
143A PRO* 4.3 21.5 - - + +
144A ALA 6.0 0.4 - - - +
166A VAL 5.2 5.8 - - - +
167A ALA* 6.0 0.2 - - - -
170A TYR* 4.2 29.4 - - + -
461A GLN 3.6 13.7 + - - +
462A LEU* 3.0 11.8 + - + +
463A ALA 2.8 3.4 + - - -
464A ARG* 1.3 76.7 - - - +
466A PHE* 1.3 57.8 + - + +
467A LYS 3.2 4.3 - - - -
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Residues in contact with PHE 466 (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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170A TYR* 5.7 6.7 - + - -
201A LYS* 2.9 46.7 + - + +
202A LEU* 5.0 13.0 - - + +
462A LEU* 3.8 15.0 - - + -
463A ALA* 3.1 5.1 + - - +
465A LEU* 1.3 76.7 - - + +
467A LYS* 1.3 73.5 + - - +
468A VAL* 4.6 10.1 - - + +
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Residues in contact with LYS 467 (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 PRO* 6.3 0.4 - - + -
201A LYS* 4.1 11.6 - - - +
463A ALA 2.7 10.3 + - - -
464A ARG* 3.3 15.0 + - + +
465A LEU 3.2 3.0 - - - -
466A PHE* 1.3 84.2 - - - +
468A VAL* 1.3 58.5 + - - +
469A ASP* 3.4 4.5 - - - +
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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