Contacts of the helix formed by residues 461 - 475 (chain C) in PDB entry 4U1D
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 461 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460C LEU* 1.3 79.9 - - - +
462C ALA* 1.3 66.1 + - - +
463C TRP* 3.1 47.4 + - - -
464C ASP* 3.2 17.2 + - - +
465C ILE* 3.1 16.5 + - - +
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Residues in contact with ALA 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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449C TYR* 4.2 19.6 - - + -
460C LEU 3.7 1.0 + - - -
461C SER* 1.3 72.2 - - - +
463C TRP* 1.3 72.2 + - + +
465C ILE* 3.3 15.5 + - - +
466C GLU* 3.2 20.3 + - - +
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Residues in contact with TRP 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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66B LYS 5.0 1.6 - - - -
69B LYS* 3.8 27.5 - - + +
70B ASP* 3.9 43.5 - - + -
73B HIS* 3.5 53.4 - + + +
163B ARG* 6.1 0.8 - - - +
164B ALA* 6.2 1.2 - - - +
167B ASP* 5.3 10.8 - - + +
170B ARG* 3.3 20.5 + - - +
461C SER* 3.1 28.2 + - - -
462C ALA* 1.3 84.0 - - + +
464C ASP* 1.3 84.4 + - - +
465C ILE 3.1 1.6 - - - -
466C GLU* 3.4 5.4 + - - +
467C LYS* 3.0 22.7 + - - +
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Residues in contact with ASP 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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163B ARG* 4.6 14.8 + - - -
167B ASP* 4.4 4.3 - - - +
460C LEU* 3.9 28.1 - - + +
461C SER* 3.2 20.8 + - - +
463C TRP* 1.3 92.3 + - - +
465C ILE* 1.3 58.3 + - - +
467C LYS* 3.2 28.9 + - + +
468C SER* 3.0 28.6 + - - -
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Residues in contact with ILE 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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429C MET* 4.3 8.5 - - + -
433C PHE* 3.5 18.3 - - + -
449C TYR* 3.5 36.3 - - + +
452C ALA* 4.1 4.9 - - + +
453C THR* 3.1 36.3 - - - +
460C LEU* 3.6 30.5 - - + +
461C SER 3.1 10.4 + - - +
462C ALA* 3.3 14.8 - - + +
463C TRP 3.1 0.2 - - - -
464C ASP* 1.3 74.0 - - - +
466C GLU* 1.3 65.8 + - - +
468C SER* 3.0 9.1 + - - -
469C LEU 3.0 17.2 + - - -
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Residues in contact with GLU 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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77B LYS* 4.4 5.7 + - - -
170B ARG* 4.5 12.1 + - - +
445C GLN* 3.1 14.6 + - - -
449C TYR* 2.6 45.1 + - + +
462C ALA 3.2 7.3 + - - +
463C TRP* 3.4 7.8 + - - +
465C ILE* 1.3 77.9 - - - +
467C LYS* 1.3 62.5 + - - +
469C LEU* 3.1 6.1 + - - +
470C LEU* 3.1 32.4 + - + +
482C ILE* 4.5 11.9 - - + +
484C HIS* 3.2 27.1 + - - -
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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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163B ARG* 4.0 15.6 - - - +
167B ASP* 2.7 37.1 + - - +
170B ARG* 3.1 28.3 - - - +
205B MET* 4.6 10.0 - - - +
208B GLN* 3.6 25.8 - - - +
209B HIS* 4.8 6.5 - - - -
463C TRP 3.0 10.2 + - - +
464C ASP* 3.2 26.9 + - - +
466C GLU* 1.3 78.2 - - - +
468C SER* 1.3 60.7 + - - +
470C LEU* 3.5 5.7 + - - +
471C GLN* 3.2 22.7 + - - +
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Residues in contact with SER 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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426C ASP* 5.8 0.3 + - - -
429C MET* 4.2 12.6 - - - +
430C ARG* 5.1 1.7 + - - -
433C PHE* 3.5 17.8 - - - -
460C LEU* 4.4 11.1 - - - +
464C ASP 3.0 14.3 + - - -
465C ILE 3.0 8.5 + - - -
467C LYS* 1.3 74.1 - - - +
469C LEU* 1.3 64.9 + - - +
471C GLN* 3.2 13.5 + - - +
472C ALA* 3.1 24.6 + - - +
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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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433C PHE* 3.4 43.0 - - + -
448C LEU* 4.0 19.5 - - + -
449C TYR* 3.8 24.2 - - + -
465C ILE 3.0 8.5 + - - +
466C GLU* 3.1 11.1 + - - +
468C SER* 1.3 76.3 - - - +
470C LEU* 1.3 61.2 + - - +
472C ALA* 3.5 3.3 + - - +
473C ALA* 3.2 18.9 + - - +
478C VAL* 4.5 4.4 - - + +
480C ILE* 3.6 25.1 - - + -
482C ILE* 3.9 21.5 - - + -
489C VAL* 4.2 5.4 - - + -
491C PHE* 4.9 5.4 - - + -
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Residues in contact with LEU 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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170B ARG* 6.4 1.8 - - - -
171B ASN* 5.4 1.8 - - - +
212B ALA* 4.0 24.2 - - + -
215B TYR* 5.0 11.9 - - + -
216B GLN* 3.4 30.5 - - + +
466C GLU* 3.1 22.7 + - + +
467C LYS* 3.9 6.1 - - - +
469C LEU* 1.3 74.0 - - - +
471C GLN* 1.3 61.1 + - - +
473C ALA* 3.1 6.3 + - + +
474C VAL* 2.9 34.1 + - + +
480C ILE* 3.8 12.6 - - + -
482C ILE* 3.7 30.7 - - + -
484C HIS* 6.3 0.4 - - + +
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Residues in contact with GLN 471 (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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208B GLN* 4.5 24.5 + - - +
336C GLN* 5.4 6.3 - - - +
430C ARG* 4.1 12.6 - - - +
467C LYS* 3.2 12.9 + - - +
468C SER* 3.5 17.4 + - - +
470C LEU* 1.3 78.2 - - - +
472C ALA* 1.3 58.2 + - - +
474C VAL* 3.1 9.6 + - + +
475C GLU* 3.0 50.4 + - + +
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Residues in contact with ALA 472 (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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430C ARG* 3.5 37.8 - - - +
433C PHE* 4.7 11.4 - - + -
434C VAL* 6.3 0.2 - - + -
468C SER 3.1 12.5 + - - +
469C LEU* 3.6 11.4 - - - +
471C GLN* 1.3 75.3 - - - +
473C ALA* 1.3 59.5 + - - +
475C GLU 3.5 1.8 + - - +
476C ASP 3.1 3.5 + - - -
477C TYR* 2.9 29.8 + - + +
478C VAL* 3.8 14.4 - - + -
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Residues in contact with ALA 473 (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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215B TYR* 3.3 42.2 - - + +
469C LEU 3.2 6.5 + - - +
470C LEU* 3.1 10.9 + - + +
472C ALA* 1.3 79.0 - - - +
474C VAL* 1.3 64.3 + - - +
476C ASP* 3.1 14.7 + - - +
478C VAL* 3.2 17.2 - - + +
480C ILE* 3.7 22.7 - - + -
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Residues in contact with VAL 474 (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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201A ARG* 3.4 15.9 + - - -
211B ASP* 4.0 35.9 - - + +
212B ALA* 4.5 6.3 - - + -
215B TYR* 3.9 30.0 - - + -
343C ILE* 6.1 3.3 - - + +
470C LEU* 2.9 22.4 + - + +
471C GLN* 3.1 10.7 + - + +
473C ALA* 1.3 77.3 - - - +
475C GLU* 1.3 62.7 + - + +
476C ASP* 3.1 3.9 + - - +
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Residues in contact with GLU 475 (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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201A ARG* 3.5 19.7 + - - +
336C GLN* 5.3 6.2 + - - -
340C ILE* 4.0 3.8 - - - +
343C ILE* 5.1 19.5 - - + +
430C ARG* 2.9 33.2 + - - +
471C GLN* 3.0 33.1 + - + +
472C ALA 3.5 1.5 + - - +
473C ALA 3.3 0.2 - - - -
474C VAL* 1.3 80.1 - - + +
476C ASP* 1.3 69.3 + - - +
477C TYR* 3.3 23.0 + - + -
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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