Contacts of the helix formed by residues 520 - 531 (chain A) in PDB entry 4G0U
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 520 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A ILE* 5.7 0.4 - - - +
507A LEU* 3.8 27.5 + - + +
516A GLN 3.1 17.7 + - - +
517A ILE 3.6 6.5 + - - +
518A MET 3.5 2.4 - - - -
519A GLU* 1.3 75.7 - - - +
521A ALA* 1.3 65.8 + - - +
522A GLU* 3.1 18.1 + - - +
523A ILE* 2.8 39.1 + - + +
524A ASN* 3.0 26.0 + - - -
13F G 4.2 2.4 + - - -
14F C 2.9 31.4 + - - +
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Residues in contact with ALA 521 (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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519A GLU 3.3 5.7 + - - +
520A ASN* 1.3 75.2 - - - +
522A GLU* 1.3 63.3 + - - +
524A ASN* 4.5 1.3 - - - +
525A ASN* 2.6 38.6 + - - +
13F G 5.9 0.6 + - - -
101F ASW 3.6 38.4 - - + +
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Residues in contact with GLU 522 (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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455A PRO* 4.9 1.7 - - - +
500A PHE* 4.9 6.3 - - + -
502A LEU* 4.5 21.0 - - + -
503A ARG 5.3 0.3 + - - -
506A ILE* 4.1 24.4 - - + +
520A ASN* 3.1 14.9 + - - +
521A ALA* 1.3 78.3 - - - +
523A ILE* 1.3 66.9 + - + +
525A ASN* 3.3 6.4 + - - +
526A ILE* 3.0 32.2 + - + +
13F G 5.8 3.6 - - - +
101F ASW 2.8 68.7 + - + +
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Residues in contact with ILE 523 (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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506A ILE* 5.0 11.9 - - + -
507A LEU* 4.6 10.3 - - + +
509A VAL* 3.8 19.3 - - + -
517A ILE* 4.4 7.2 - - + +
520A ASN* 2.8 35.8 + - + +
522A GLU* 1.3 75.5 - - + +
524A ASN* 1.3 67.4 + - - +
526A ILE* 3.1 7.3 + - + +
527A ILE* 2.9 29.0 + - + +
534A TYR* 3.5 24.9 - - - +
572A PHE* 3.6 45.0 - - + -
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Residues in contact with ASN 524 (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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517A ILE 3.5 12.5 + - - +
518A MET* 2.8 36.4 + - - +
519A GLU 3.9 1.6 - - - -
520A ASN 3.0 22.3 + - - +
521A ALA* 4.5 1.6 - - - +
523A ILE* 1.3 85.9 - - - +
525A ASN* 1.3 62.3 + - - +
527A ILE* 3.7 13.5 - - - +
528A LYS* 3.0 45.1 + - - +
534A TYR* 4.5 4.3 + - - -
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Residues in contact with ASN 525 (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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455A PRO* 5.5 2.8 + - - +
500A PHE* 3.7 31.1 - - + -
521A ALA* 2.6 40.0 + - - +
522A GLU* 3.7 5.0 + - - +
523A ILE 3.2 0.2 - - - -
524A ASN* 1.3 77.7 - - - +
526A ILE* 1.3 58.8 + - - +
528A LYS* 3.8 10.3 + - - +
529A ILE* 3.0 39.0 + - + +
101F ASW 4.7 9.3 - - - +
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Residues in contact with ILE 526 (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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473A LEU* 5.1 2.9 - - + -
475A LEU* 4.2 13.2 - - + -
500A PHE* 4.3 14.1 - - + -
502A LEU* 4.2 15.9 - - + -
506A ILE* 5.6 2.7 - - + -
522A GLU* 3.0 20.3 + - + +
523A ILE* 3.5 10.1 - - + +
525A ASN* 1.3 76.2 - - - +
527A ILE* 1.3 63.3 + - - +
529A ILE* 3.5 6.2 + - - +
530A VAL* 3.1 36.0 + - + +
532A LEU* 4.5 3.8 - - + +
552A ILE* 4.5 14.6 - - + -
569A LEU* 4.0 26.9 - - + -
572A PHE* 4.3 20.4 - - + -
573A ILE* 5.6 0.2 - - + -
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Residues in contact with ILE 527 (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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523A ILE* 2.9 26.7 + - + +
524A ASN* 3.7 12.6 - - - +
525A ASN 3.3 0.2 - - - -
526A ILE* 1.3 76.3 - - - +
528A LYS* 1.3 56.5 + - + +
531A GLY* 2.7 31.2 + - - -
532A LEU* 3.0 38.7 + - + +
533A GLN* 5.3 0.9 - - - -
534A TYR* 3.3 46.2 - - + +
572A PHE* 4.0 12.1 - - + -
577A TRP* 4.1 14.8 - - + -
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Residues in contact with LYS 528 (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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524A ASN* 3.0 35.8 + - - +
525A ASN* 3.8 11.2 + - - +
527A ILE* 1.3 78.7 - - + +
529A ILE* 1.3 64.2 + - + +
531A GLY* 3.1 12.3 + - - -
548A ARG* 3.8 9.2 - - - -
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Residues in contact with ILE 529 (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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457A LEU* 3.7 34.1 - - + -
473A LEU* 3.7 23.6 - - + -
500A PHE* 3.8 40.8 - - + -
525A ASN* 3.0 25.2 + - + +
526A ILE* 4.0 4.5 - - - +
527A ILE 3.4 0.2 - - - -
528A LYS* 1.3 77.3 - - + +
530A VAL* 1.3 57.1 + - - +
548A ARG* 2.7 32.5 + - - +
549A TYR* 3.5 25.7 - - + -
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Residues in contact with VAL 530 (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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473A LEU* 3.8 24.5 - - + -
526A ILE* 3.1 19.4 + - + +
529A ILE* 1.3 79.8 - - + +
531A GLY* 1.3 63.9 + - - +
532A LEU* 4.0 17.7 - - + -
547A LEU* 3.3 6.7 - - + -
548A ARG* 2.8 25.1 + - - -
549A TYR* 4.0 27.4 - - + +
552A ILE* 4.2 16.4 - - + -
585A PHE* 3.9 26.2 - - + -
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Residues in contact with GLY 531 (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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527A ILE 2.7 8.4 + - - -
528A LYS* 3.1 11.0 + - - -
530A VAL* 1.3 80.7 - - - +
532A LEU* 1.3 64.8 + - - +
533A GLN* 3.9 10.0 - - - +
538A TYR* 4.1 0.2 + - - -
546A THR* 4.2 12.6 + - - +
547A LEU* 3.6 11.0 - - - +
548A ARG* 4.1 10.5 - - - +
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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