Contacts of the helix formed by residues 455 - 467 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387C LYS* 4.3 5.0 + - - +
388C GLY* 3.6 17.5 + - - -
389C TYR* 4.9 9.0 - - - +
452C LEU 4.9 1.7 + - - -
454C LEU* 1.3 80.3 + - - +
456C GLU* 1.3 55.4 + - - +
457C GLU 3.8 1.1 - - - -
458C GLN* 3.1 11.8 - - - +
459C LEU* 2.8 35.8 + - - +
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Residues in contact with GLU 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C TYR* 4.8 9.2 - - - +
406C PRO* 4.7 19.6 - - + +
455C SER* 1.3 74.7 - - - +
457C GLU* 1.3 54.2 + - + +
459C LEU* 3.0 9.1 + - - +
460C GLU* 2.6 45.0 + - + +
472C ASN* 4.9 17.3 - - + -
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Residues in contact with GLU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455C SER 3.8 0.2 - - - -
456C GLU* 1.3 76.4 - - + +
458C GLN* 1.3 60.4 - - - +
460C GLU* 3.6 13.7 - - + -
461C GLN* 3.0 47.5 + - + +
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Residues in contact with GLN 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ASP* 3.6 36.7 - - + -
165C HIS* 6.4 0.4 - - + -
166C VAL* 3.7 28.7 - - + +
453C ALA 5.9 0.2 - - - +
454C LEU* 4.4 24.7 - - + +
455C SER 3.1 19.3 - - - +
457C GLU* 1.3 79.1 - - - +
459C LEU* 1.3 62.7 + - - +
461C GLN* 3.8 7.5 + - - +
462C LEU* 4.0 2.8 + - - +
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Residues in contact with LEU 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C LEU* 6.2 3.8 - - + -
389C TYR* 4.6 17.9 - - + -
391C ILE* 5.2 12.1 - - + -
451C THR* 6.2 2.7 - - - -
454C LEU* 4.7 20.8 - - + +
455C SER 2.8 14.3 + - - +
456C GLU* 3.4 8.3 - - - +
458C GLN* 1.3 74.6 - - - +
460C GLU* 1.3 66.3 + - - +
462C LEU* 3.3 12.9 + - - +
463C ALA* 3.5 12.5 + - - +
470C PHE* 5.1 4.2 - - + -
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Residues in contact with GLU 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456C GLU* 2.6 28.9 + - + +
457C GLU* 3.4 20.6 - - + +
459C LEU* 1.3 74.1 - - - +
461C GLN* 1.3 63.5 + - + +
462C LEU 3.1 1.7 + - - -
463C ALA* 3.4 3.8 + - - +
464C ARG* 3.2 20.8 + - - +
470C PHE* 4.6 21.9 - - + +
472C ASN* 5.5 7.0 - - - -
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Residues in contact with GLN 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C PRO 4.8 2.8 - - - +
145C ALA* 3.3 26.4 - - + +
159C GLN* 5.3 2.8 + - - +
162C ASP* 4.1 19.8 - - - -
163C TRP* 3.2 42.7 - - + +
166C VAL* 5.1 4.8 - - + +
457C GLU* 3.0 33.9 + - + +
458C GLN* 4.0 6.5 - - - +
459C LEU 3.3 0.4 - - - -
460C GLU* 1.3 80.4 - - + +
462C LEU* 1.3 58.0 + - + +
464C ARG* 3.3 20.1 - - - +
465C LEU* 3.4 16.3 + - - +
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Residues in contact with LEU 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C VAL* 4.2 33.0 - - + +
169C ALA* 5.2 9.2 - - + -
170C TYR* 5.3 6.1 - - + +
458C GLN 4.0 5.3 + - - +
459C LEU* 3.3 8.1 + - - +
460C GLU 3.2 0.6 - - - -
461C GLN* 1.3 76.5 - - - +
463C ALA* 1.3 67.7 + - - +
464C ARG 3.0 0.9 - - - -
465C LEU* 2.8 21.3 + - + +
466C PHE* 3.0 19.8 + - + -
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Residues in contact with ALA 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C PHE* 4.7 16.4 - - + -
459C LEU 3.5 7.8 + - - +
460C GLU 3.4 8.2 + - - +
462C LEU* 1.3 76.6 - - - +
464C ARG* 1.3 52.9 + - - +
466C PHE* 3.3 6.3 + - - +
467C LYS* 2.6 36.7 + - - -
468C VAL* 3.3 16.5 + - + +
470C PHE* 3.9 27.8 - - + -
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Residues in contact with ARG 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C PRO* 3.5 31.0 - - + +
144C ALA 5.6 0.9 - - - +
460C GLU 3.2 11.7 + - - +
461C GLN* 3.3 17.0 - - - +
463C ALA* 1.3 78.6 - - - +
465C LEU* 1.3 57.5 + - - +
467C LYS* 3.7 15.8 + - - +
468C VAL 5.5 0.4 - - - -
470C PHE* 5.8 0.2 - - - +
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Residues in contact with LEU 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C PRO* 5.2 12.3 - - + -
143C PRO* 4.1 22.8 - - + +
163C TRP* 5.1 14.4 - - + +
166C VAL* 5.4 6.5 - - + +
167C ALA* 6.2 0.2 - - - -
170C TYR* 4.5 25.7 - - + -
461C GLN 3.4 14.4 + - - +
462C LEU* 2.8 14.6 + - + +
464C ARG* 1.3 79.1 - - - +
466C PHE* 1.3 64.6 + - + +
467C LYS* 3.7 1.4 + - - +
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Residues in contact with PHE 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C TYR* 5.3 12.1 - + + -
201C LYS* 2.9 43.2 + - - +
202C LEU* 4.8 12.3 - - + -
462C LEU* 3.0 18.9 + - + +
463C ALA* 3.7 9.0 - - - +
465C LEU* 1.3 76.1 - - + +
467C LYS* 1.3 62.5 + - - +
468C VAL* 4.1 15.7 - - + -
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Residues in contact with LYS 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C LYS* 4.2 13.3 - - - +
463C ALA 2.6 15.9 + - - -
464C ARG* 4.0 13.5 - - - +
465C LEU 3.3 2.9 - - - +
466C PHE* 1.3 76.8 - - - +
468C VAL* 1.3 62.3 + - - +
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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