Contacts of the helix formed by residues 486 - 499 (chain A) in PDB entry 4UHW
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 ASN 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A HIS* 3.5 2.8 + - + -
485A TRP* 1.3 76.8 - - - +
487A GLU* 1.3 69.1 + - - +
488A GLN* 3.2 28.2 + - - +
489A MET* 3.0 30.1 + - - +
490A LEU* 3.6 2.8 - - - +
527A TYR* 2.8 32.6 + - - -
543A PRO* 4.9 14.3 - - - +
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Residues in contact with GLU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A ASN* 1.3 78.4 - - - +
488A GLN* 1.3 64.5 + - - +
489A MET 3.2 0.2 - - - -
490A LEU* 3.3 21.3 + - + +
491A ASP* 3.4 21.8 + - - +
524A PHE* 5.0 3.6 - - - -
527A TYR* 3.7 27.4 - - + +
549A TYR* 4.8 15.8 + - - -
1318A LYS* 4.3 17.6 + - - +
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Residues in contact with GLN 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ARG* 5.7 4.5 - - - +
484A HIS* 3.8 20.3 + - - +
485A TRP 4.2 0.4 - - - -
486A ASN* 3.1 53.4 + - - +
487A GLU* 1.3 78.9 - - - +
489A MET* 1.3 63.6 + - + +
490A LEU 3.7 0.2 + - - -
491A ASP* 4.0 4.9 + - - +
492A ILE* 3.8 24.2 + - + +
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Residues in contact with MET 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A LEU* 6.2 0.9 - - - -
480A LEU* 4.3 13.1 - - + +
483A ARG* 4.0 24.5 - - + -
484A HIS 3.6 18.2 - - - +
485A TRP* 3.4 52.0 - - + -
486A ASN 3.0 18.2 + - - +
488A GLN* 1.3 79.7 - - - +
490A LEU* 1.3 75.6 + - + +
492A ILE* 3.2 11.4 - - + +
493A ALA* 2.7 46.1 + - - +
527A TYR* 4.5 1.6 - - + -
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A ASN 3.6 14.1 - - - +
487A GLU* 3.3 14.8 + - + +
489A MET* 1.3 91.2 - - + +
491A ASP* 1.3 61.6 + - - +
493A ALA* 4.2 5.2 - - - -
494A CYS* 2.8 47.2 + - - -
523A LEU* 5.3 6.3 - - + +
524A PHE* 3.8 28.3 - - + +
527A TYR* 3.3 59.0 - - + -
1318A LYS* 5.7 4.3 - - - +
1319A PHE* 5.5 4.9 - - + -
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Residues in contact with ASP 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A GLU* 3.4 16.2 + - - +
488A GLN* 4.3 4.6 - - - +
489A MET 3.5 0.2 - - - -
490A LEU* 1.3 80.7 - - - +
492A ILE* 1.3 65.1 + - + +
494A CYS* 3.7 6.5 + - - +
495A ARG* 3.3 27.1 + - - +
1318A LYS* 4.5 21.8 + - - +
1322A MET* 4.7 15.0 - - + +
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Residues in contact with ILE 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A LEU* 4.5 5.8 - - + -
483A ARG* 3.3 50.3 - - - +
488A GLN 3.8 9.6 + - - +
489A MET* 3.2 18.2 - - - +
491A ASP* 1.3 77.7 - - + +
493A ALA* 1.3 62.7 + - - +
495A ARG* 3.2 9.0 + - + +
496A LEU* 2.9 39.0 + - + +
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Residues in contact with ALA 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A LEU* 3.8 24.9 - - + -
489A MET* 2.7 30.8 + - - +
490A LEU* 3.7 5.4 - - - +
492A ILE* 1.3 72.9 - - - +
494A CYS* 1.3 56.9 + - - +
496A LEU* 3.3 11.2 + - - +
497A ILE* 2.9 36.1 + - + +
523A LEU* 4.1 17.7 - - + -
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Residues in contact with CYS 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A LEU* 2.8 36.8 + - - +
491A ASP* 3.8 2.9 - - - +
493A ALA* 1.3 69.6 - - - +
495A ARG* 1.3 65.2 + - - +
497A ILE* 3.5 8.7 - - - +
498A LEU* 3.0 31.0 + - - +
520A ILE* 4.0 21.3 - - + -
523A LEU* 3.8 17.7 - - - +
524A PHE 5.9 0.7 - - - -
1319A PHE* 4.5 15.3 - - - -
1322A MET* 3.4 29.6 - - - -
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Residues in contact with ARG 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A ASP 3.3 15.6 + - - +
492A ILE* 3.2 11.5 + - - +
494A CYS* 1.3 81.5 - - - +
496A LEU* 1.3 59.4 + - + +
498A LEU* 3.2 14.9 + - - +
499A ASN* 2.9 23.6 + - - +
1322A MET* 3.6 45.8 + - + +
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Residues in contact with LEU 496 (chain A).
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* 2.6 55.4 + - - +
479A LYS* 3.9 39.3 - - + +
480A LEU* 4.5 11.0 - - + -
483A ARG* 5.9 1.3 - - - +
492A ILE* 2.9 28.1 + - + +
493A ALA* 3.4 21.3 - - - +
495A ARG* 1.3 76.5 - - + +
497A ILE* 1.3 55.8 + - + +
499A ASN* 3.1 17.6 - - - +
500A GLU* 3.6 8.3 - - - +
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Residues in contact with ILE 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ILE* 5.1 12.3 - - + -
463A TYR* 3.6 17.3 - - + +
473A ALA* 4.4 10.8 - - + -
476A SER* 3.5 24.0 - - - +
480A LEU* 5.8 1.1 - - + -
493A ALA* 2.9 25.9 + - + +
494A CYS* 3.5 8.5 - - - +
496A LEU* 1.3 74.0 - - + +
498A LEU* 1.3 62.3 + - - +
499A ASN 3.1 2.7 - - - -
500A GLU* 3.1 2.0 + - - -
501A VAL* 2.8 44.8 + - + +
519A ILE* 3.4 32.8 - - + +
520A ILE* 4.2 5.2 - - + -
523A LEU* 3.7 22.4 - - + -
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Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494A CYS 3.0 25.4 + - - +
495A ARG* 3.2 8.2 + - - +
497A ILE* 1.3 76.7 - - - +
499A ASN* 1.3 55.5 + - - +
501A VAL* 4.2 4.4 - - - +
502A SER* 3.6 20.4 - - - -
516A ARG* 3.7 26.1 - - + +
519A ILE* 4.8 7.6 - - + -
520A ILE* 3.5 32.1 - - + -
1322A MET* 3.9 28.5 - - + +
1323A ILE* 4.4 2.7 - - + -
1324A PRO* 4.0 42.1 - - + +
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Residues in contact with ASN 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ARG* 2.9 20.3 + - - +
496A LEU* 3.1 20.9 - - - +
498A LEU* 1.3 74.3 - - - +
500A GLU* 1.3 63.7 + - - +
502A SER* 3.9 14.0 + - - -
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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