Contacts of the helix formed by residues 461 - 470 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435D ILE* 4.0 30.7 - - + +
438D LEU* 4.5 13.5 - - + +
439D ARG* 3.8 43.3 - - + +
443D PHE 4.5 11.4 - - - +
444D ASN* 2.9 26.3 + - + +
460D THR* 1.3 72.9 - - - +
462D GLY* 1.3 58.2 + - - +
464D MET* 3.2 7.9 + - - +
465D LEU* 3.0 46.0 + - + +
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Residues in contact with GLY 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B SER* 4.2 7.0 - - - -
200B PRO* 4.1 20.7 - - - +
444D ASN 4.8 0.2 + - - -
460D THR* 3.3 2.6 + - - -
461D LEU* 1.3 78.0 - - - +
463D ASN* 1.3 60.6 + - - +
465D LEU* 3.3 11.1 + - - +
466D SER* 2.9 30.0 + - - -
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Residues in contact with ASN 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ASN* 4.4 5.7 + - - +
195B ALA* 4.0 0.2 - - - -
196B ARG* 3.3 32.7 + - - +
199B SER* 3.8 8.5 + - - -
201B GLU* 4.0 2.4 + - - +
460D THR* 3.1 25.0 + - - +
461D LEU 3.3 0.4 - - - -
462D GLY* 1.3 77.1 - - - +
464D MET* 1.3 53.9 + - + +
466D SER* 3.8 0.8 - - - -
467D SER* 2.5 39.8 + - - -
482D VAL* 3.5 26.7 + - - +
484D TYR* 3.1 34.4 + - - +
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Residues in contact with MET 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431D CYS* 4.0 21.5 - - - +
434D THR* 3.8 17.7 - - - -
435D ILE* 3.9 30.3 - - + -
438D LEU* 5.4 1.8 - - - -
459D VAL* 3.5 28.7 - - + -
460D THR 3.3 11.8 + - - +
461D LEU* 3.2 11.2 + - - +
462D GLY 3.2 0.2 - - - -
463D ASN* 1.3 78.1 - - + +
465D LEU* 1.3 66.0 - - - +
467D SER* 3.2 6.2 + - - -
468D LEU* 2.9 30.6 + - + +
473D VAL* 4.8 1.0 - - - +
479D VAL* 3.5 31.0 - - + -
482D VAL* 4.3 14.4 - - + -
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Residues in contact with LEU 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D ILE* 4.2 26.2 - - + -
439D ARG* 5.1 8.3 - - - +
461D LEU* 3.0 37.6 + - + +
462D GLY* 3.6 11.0 - - - +
464D MET* 1.3 74.9 - - - +
466D SER* 1.3 64.3 + - - +
468D LEU* 3.1 7.5 + - + +
469D LEU* 2.9 38.9 + - + +
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Residues in contact with SER 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ARG* 3.1 30.1 + - - +
198B ASP* 3.2 31.5 + - - +
199B SER* 4.5 3.4 - - - -
462D GLY 2.9 16.8 + - - -
463D ASN* 3.8 5.2 - - - -
465D LEU* 1.3 77.4 - - - +
467D SER* 1.3 63.4 + - - +
469D LEU* 3.4 8.4 + - - +
470D ALA* 3.1 23.9 + - - +
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Residues in contact with SER 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ARG* 3.9 10.7 - - - +
463D ASN* 2.5 32.0 + - - -
464D MET* 3.2 4.9 + - - -
466D SER* 1.3 77.8 - - - +
468D LEU* 1.3 58.7 + - - +
470D ALA* 3.6 2.5 + - - -
471D GLY 3.3 1.7 + - - -
472D LYS* 3.0 40.2 + - - +
473D VAL* 3.5 19.5 + - - -
482D VAL* 3.8 20.3 - - - +
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Residues in contact with LEU 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A GLN* 5.9 2.6 - - - +
431D CYS* 5.1 5.2 - - + -
432D GLY* 5.6 0.2 - - - -
435D ILE* 3.6 30.7 - - + -
464D MET* 2.9 17.7 + - + +
465D LEU* 3.6 8.7 - - + +
467D SER* 1.3 74.9 - - - +
469D LEU* 1.3 64.9 + - + +
470D ALA 3.0 1.6 - - - -
471D GLY* 2.9 19.8 + - - -
473D VAL* 3.2 31.5 - - + +
474D GLN 3.6 22.4 - - - +
475D PRO* 3.6 21.8 - - + -
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Residues in contact with LEU 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A SER* 5.8 0.5 + - - -
465D LEU* 2.9 30.2 + - + +
466D SER* 3.9 7.4 - - - +
468D LEU* 1.3 81.2 - - + +
470D ALA* 1.3 59.5 + - - +
471D GLY 3.5 0.2 + - - -
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Residues in contact with ALA 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ARG* 3.6 22.4 - - - +
466D SER 3.1 17.1 + - - +
467D SER 3.8 0.4 - - - +
468D LEU 3.0 0.6 - - - -
469D LEU* 1.3 79.7 - - - +
471D GLY* 1.3 58.0 + - - +
472D LYS* 3.1 42.8 + - + +
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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