Contacts of the helix formed by residues 461 - 470 (chain C) in PDB entry 4L28
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 461 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435C ILE* 4.4 24.2 - - + +
438C LEU* 4.3 15.3 - - + +
439C ARG* 4.0 44.6 - - + +
443C PHE 4.4 11.7 - - - +
444C ASN* 2.9 33.5 + - + +
460C THR* 1.3 71.4 - - - +
462C GLY* 1.3 58.6 + - - +
464C MET* 3.2 7.1 + - - +
465C LEU* 3.0 42.4 + - + +
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Residues in contact with GLY 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 4.3 7.0 - - - -
200A PRO* 4.2 15.2 - - - +
460C THR* 3.3 8.7 - - - +
461C LEU* 1.3 79.2 - - - +
463C ASN* 1.3 60.0 + - - +
465C LEU* 3.4 10.7 + - - +
466C SER* 2.9 29.6 + - - -
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Residues in contact with ASN 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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194A ASN* 4.3 4.9 + - - +
196A ARG* 3.1 33.6 + - - +
199A SER* 3.8 10.9 - - - -
460C THR* 3.6 17.3 - - + +
461C LEU 3.3 0.8 - - - -
462C GLY* 1.3 76.9 - - - +
464C MET* 1.3 55.3 - - + +
466C SER* 3.7 1.5 - - - -
467C SER* 2.7 40.0 + - - -
482C VAL* 3.6 25.3 + - - +
484C TYR* 3.1 43.6 + - + +
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Residues in contact with MET 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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431C CYS* 3.3 48.2 - - + +
434C THR* 4.6 5.6 - - - +
435C ILE* 4.0 18.6 - - + -
459C VAL* 4.6 11.2 - - + -
460C THR 3.2 14.6 + - - +
461C LEU* 3.4 10.3 - - - +
463C ASN* 1.3 77.6 - - + +
465C LEU* 1.3 66.8 + - - +
466C SER 3.1 1.1 - - - -
467C SER* 3.2 2.7 + - - +
468C LEU* 2.9 36.5 + - + +
473C VAL* 5.1 1.3 - - + -
479C VAL* 5.7 1.6 - - - -
482C VAL* 3.3 39.5 - - + -
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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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435C ILE* 4.0 32.8 - - + -
439C ARG* 3.4 31.0 - - - +
461C LEU* 3.0 31.8 + - + +
462C GLY* 3.4 7.6 + - - +
464C MET* 1.3 75.9 - - - +
466C SER* 1.3 58.3 + - - +
468C LEU* 3.8 5.6 - - + +
469C LEU* 2.9 34.4 + - - +
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Residues in contact with SER 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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196A ARG* 3.0 28.2 + - - +
198A ASP* 3.1 32.2 + - - +
199A SER* 4.6 2.7 - - - -
462C GLY 2.9 18.4 + - - -
463C ASN* 3.7 5.2 - - - -
465C LEU* 1.3 78.2 - - - +
467C SER* 1.3 61.0 - - - +
469C LEU* 4.0 7.3 - - - +
470C ALA* 3.1 25.8 + - - +
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Residues in contact with SER 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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196A ARG* 3.6 18.3 - - - +
463C ASN* 2.7 24.7 + - - -
464C MET 3.2 3.6 + - - -
466C SER* 1.3 77.1 - - - +
468C LEU* 1.3 60.0 + - - +
470C ALA 3.6 0.3 + - - -
471C GLY 3.3 1.6 + - - -
472C LYS* 2.9 42.3 + - - +
473C VAL* 3.4 20.4 + - - -
482C VAL* 3.9 18.4 - - - +
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Residues in contact with LEU 468 (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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431C CYS* 5.1 0.2 - - + -
432C GLY* 5.3 0.7 - - - -
435C ILE* 3.5 32.5 - - + -
464C MET* 2.9 22.9 + - + +
465C LEU* 3.8 6.3 - - + +
467C SER* 1.3 75.6 - - - +
469C LEU* 1.3 64.1 + - - +
470C ALA 3.1 1.8 - - - -
471C GLY* 3.0 14.0 + - - -
473C VAL* 3.2 33.1 - - + +
474C GLN 3.5 4.3 - - - +
475C PRO* 3.5 40.6 - - + -
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Residues in contact with LEU 469 (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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465C LEU 2.9 18.2 + - - +
466C SER* 4.0 6.5 - - - +
468C LEU* 1.3 78.1 - - - +
470C ALA* 1.3 59.9 + - - +
471C GLY 3.5 0.5 + - - -
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Residues in contact with ALA 470 (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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196A ARG* 3.3 31.9 - - - +
466C SER 3.1 18.2 + - - +
467C SER 4.0 4.0 - - - +
468C LEU 3.1 1.0 - - - -
469C LEU* 1.3 79.3 - - - +
471C GLY* 1.3 58.7 + - - +
472C LYS* 3.4 18.7 + - + +
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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