Contacts of the helix formed by residues 458 - 467 (chain E) 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 GLN 458 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158E GLU* 5.5 2.0 - - - +
162E ASP* 3.2 29.4 - - + +
166E VAL* 3.0 29.2 - - + +
454E LEU* 3.9 23.8 - - + -
455E SER* 2.5 40.8 + - - +
457E GLU* 1.3 76.3 - - + +
459E LEU* 1.3 57.0 + - - +
460E GLU 3.4 0.2 - - - -
461E GLN* 3.6 13.5 - - - +
462E LEU* 4.3 0.5 + - - +
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Residues in contact with LEU 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E LEU* 5.8 7.4 - - + -
389E TYR* 5.6 10.5 - - + -
454E LEU* 5.0 16.8 - - + -
455E SER 2.6 20.4 + - - +
456E GLU* 3.8 5.6 - - - +
458E GLN* 1.3 74.5 - - - +
460E GLU* 1.3 58.0 + - - +
461E GLN 3.1 5.5 + - - +
462E LEU* 4.4 11.6 + - + +
463E ALA* 4.5 8.7 + - - +
470E PHE* 4.5 13.0 - - - -
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Residues in contact with GLU 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456E GLU* 3.1 24.0 + - + +
457E GLU* 3.5 8.0 + - - +
458E GLN 3.4 1.2 - - - -
459E LEU* 1.3 78.1 - - - +
461E GLN* 1.3 59.2 + - - +
463E ALA* 5.7 0.7 - - - -
464E ARG* 3.0 32.0 - - + +
470E PHE* 5.3 12.1 - - + -
472E ASN* 5.7 9.4 - - + -
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Residues in contact with GLN 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E ALA* 4.7 12.8 - - + -
159E GLN 5.6 0.4 + - - -
162E ASP* 3.7 20.2 + - - -
163E TRP* 2.8 46.9 - - + +
166E VAL* 3.4 19.6 - - + +
457E GLU 3.5 19.4 + - - +
458E GLN* 3.6 14.1 + - - +
459E LEU 3.1 0.4 - - - -
460E GLU* 1.3 80.5 - - - +
462E LEU* 1.3 68.3 + - - +
463E ALA 3.4 0.9 - - - -
464E ARG* 3.9 2.9 - - - -
465E LEU* 2.9 34.9 + - + +
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Residues in contact with LEU 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E VAL* 4.1 27.7 - - + +
169E ALA* 5.2 7.4 - - + -
170E TYR* 4.8 12.1 - - + +
173E SER* 5.7 2.7 - - - +
317E LEU* 6.4 3.6 - - + -
458E GLN 4.3 2.1 + - - +
459E LEU* 4.4 8.2 + - + +
461E GLN* 1.3 77.9 - - - +
463E ALA* 1.3 52.9 + - - +
465E LEU* 3.1 4.6 + - - +
466E PHE* 2.6 52.8 + - + +
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Residues in contact with ALA 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402E PHE* 4.8 8.7 - - + -
459E LEU 4.5 11.1 + - - +
460E GLU* 5.5 0.9 - - - -
461E GLN 3.4 0.2 - - - -
462E LEU* 1.3 77.9 - - - +
464E ARG* 1.3 52.5 + - - +
466E PHE* 2.5 13.3 + - - -
467E LYS* 2.4 36.2 + - - -
468E VAL* 3.4 31.0 - - + +
469E ASP 4.6 0.2 - - - +
470E PHE* 4.2 20.0 - - + -
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Residues in contact with ARG 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E PRO* 3.5 17.8 - - - +
144E ALA 5.8 5.2 - - - +
460E GLU* 3.0 29.9 + - + +
461E GLN* 3.5 6.4 + - - +
462E LEU 3.4 0.4 - - - -
463E ALA* 1.3 76.3 - - - +
465E LEU* 1.3 61.7 + - + +
467E LYS* 3.7 12.6 + - - +
468E VAL 4.4 1.7 + - - -
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Residues in contact with LEU 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E PRO* 4.6 18.6 - - + -
143E PRO* 4.0 27.4 - - + +
144E ALA* 4.9 5.6 - - - +
145E ALA 5.9 0.4 - - - +
163E TRP* 5.7 5.6 - - + +
166E VAL* 6.1 3.1 - - + +
170E TYR* 5.0 18.5 - - + -
461E GLN* 2.9 30.0 + - + +
462E LEU* 3.8 2.9 - - - +
463E ALA 2.8 0.8 + - - -
464E ARG* 1.3 75.0 - - + +
466E PHE* 1.3 61.4 + - - +
467E LYS* 3.0 10.4 + - - +
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Residues in contact with PHE 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E TYR* 5.0 15.5 - + + -
173E SER* 6.2 3.4 - - - -
201E LYS* 3.3 32.3 - - - +
202E LEU* 5.5 11.2 - - + -
462E LEU* 2.6 34.8 + - + +
463E ALA* 2.5 13.4 + - - +
465E LEU* 1.3 72.6 - - - +
467E LYS* 1.3 67.9 + - - +
468E VAL* 3.3 7.1 + - + +
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Residues in contact with LYS 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E PRO* 4.6 11.2 - - + -
201E LYS* 2.4 34.7 + - - +
463E ALA 2.4 17.6 + - - -
464E ARG* 3.9 15.9 - - - +
465E LEU 3.0 7.7 - - - +
466E PHE* 1.3 71.2 - - - +
468E VAL* 1.3 53.2 + - - +
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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