Contacts of the helix formed by residues 503 - 513 (chain A) in PDB entry 5XA0
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 503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501A LYS 3.5 1.4 + - - -
502A PRO* 1.3 84.8 - - - +
504A ARG* 1.4 64.5 + - - +
505A GLU* 2.5 43.3 + - - +
506A ARG* 3.7 38.7 + - + +
507A GLN* 2.8 34.6 + - - +
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Residues in contact with ARG 504 (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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503A ASN* 1.4 80.2 + - - +
505A GLU* 1.3 69.2 + - - +
507A GLN* 4.4 3.6 - - - +
508A LYS* 3.1 31.3 + - + +
566A ASP* 3.1 34.2 - - - +
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Residues in contact with GLU 505 (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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439A GLU* 4.1 33.4 - - + +
442A ASP* 5.1 7.2 - - + +
503A ASN* 2.5 42.2 + - - +
504A ARG* 1.3 83.1 - - - +
506A ARG* 1.3 62.6 + - + +
508A LYS* 3.8 9.6 - - - +
509A LEU* 2.9 33.0 + - + +
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Residues in contact with ARG 506 (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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438A ALA* 5.0 8.7 - - - +
442A ASP* 2.5 39.6 + - - +
483A PHE* 4.4 27.9 - - + +
484A VAL* 4.4 15.9 - - - +
485A THR 4.0 21.9 + - - -
502A PRO* 4.9 1.3 - - + +
503A ASN* 3.7 42.4 - - + +
504A ARG 3.3 0.2 - - - -
505A GLU* 1.3 76.1 - - - +
507A GLN* 1.3 62.3 + - + +
509A LEU* 2.9 29.0 + - - +
510A MET* 3.4 4.7 + - - +
563A SER* 4.3 4.8 + - - +
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Residues in contact with GLN 507 (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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484A VAL 3.8 1.2 + - - -
501A LYS* 4.6 3.1 - - - -
502A PRO* 2.7 34.0 - - - +
503A ASN 2.8 20.2 - - - +
504A ARG* 4.4 3.4 - - - +
506A ARG* 1.3 69.8 - - - +
508A LYS* 1.3 67.2 + - - +
509A LEU 3.0 1.3 - - - -
510A MET* 3.2 19.2 - - - +
511A ARG* 3.9 2.9 + - - +
562A HIS* 2.8 36.2 + - - +
563A SER* 2.9 38.9 + - - +
564A GLN 3.4 1.2 + - - -
565A GLN* 3.7 11.8 + - - +
566A ASP 5.2 0.5 + - - -
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Residues in contact with LYS 508 (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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278A SER* 5.9 7.4 - - - -
504A ARG* 3.1 23.4 + - + +
505A GLU* 3.8 8.7 - - - +
507A GLN* 1.3 75.8 - - - +
509A LEU* 1.3 66.3 + - + +
511A ARG* 3.0 6.9 + - + +
512A GLU* 2.8 63.9 + - + +
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Residues in contact with LEU 509 (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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442A ASP* 3.0 36.8 - - + +
443A LEU* 3.1 29.4 - - + +
446A ALA* 2.9 17.7 - - + -
483A PHE* 5.1 5.2 - - + -
505A GLU* 2.9 17.0 + - + +
506A ARG* 2.9 18.6 + - - +
508A LYS* 1.3 74.1 - - + +
510A MET* 1.3 59.0 + - - +
512A GLU* 5.3 2.2 - - + -
513A GLN* 2.5 68.7 + - + +
515A ILE* 4.1 2.0 - - + -
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Residues in contact with MET 510 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480A LEU* 5.7 0.7 - - + -
506A ARG 3.4 3.7 + - - +
507A GLN 3.2 15.5 - - - +
509A LEU* 1.3 72.8 - - - +
511A ARG* 1.3 56.3 + - - +
513A GLN 2.5 27.9 - - - +
515A ILE* 3.0 43.9 - - + +
516A LEU* 2.6 63.7 + - + +
519A ILE* 4.2 12.3 - - + -
559A VAL* 3.4 24.2 - - + +
560A LEU* 5.4 3.6 - - - +
563A SER* 4.0 24.9 - - - +
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Residues in contact with ARG 511 (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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507A GLN 3.9 2.9 + - - +
508A LYS* 3.0 10.2 + - - +
510A MET* 1.3 73.2 - - - +
512A GLU* 1.3 85.9 + - - +
513A GLN 2.9 13.5 - - - +
516A LEU* 2.8 37.2 - - + +
517A LYS* 4.3 7.6 - - - +
569A LYS* 4.3 22.8 - - + +
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Residues in contact with GLU 512 (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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508A LYS* 2.8 55.1 + - + +
509A LEU* 5.3 2.5 - - + -
511A ARG* 1.3 112.6 + - - +
513A GLN* 1.3 63.5 + - + +
517A LYS* 5.3 1.4 - - - +
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Residues in contact with GLN 513 (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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443A LEU* 2.3 45.3 - - + +
446A ALA* 2.6 10.4 + - + +
447A ASN* 2.0 68.8 + - - +
450A SER* 3.5 1.8 + - - -
509A LEU* 2.5 28.4 + - + +
510A MET 2.5 20.8 - - - +
511A ARG 2.9 8.7 - - - +
512A GLU* 1.3 77.6 - - - +
514A ASN* 1.3 79.7 + - - +
515A ILE 3.0 3.5 + - - -
517A LYS* 3.7 6.0 - - - +
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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