Contacts of the strand formed by residues 518 - 527 (chain G) in PDB entry 5IXM
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 518 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483G GLN* 2.7 37.8 + - - -
508G ILE* 3.9 12.6 - - - -
510G GLY 3.6 4.9 - - - -
511G TRP* 3.3 10.5 - - - +
517G THR* 1.3 80.9 + - - +
519G LYS* 1.3 64.4 + - - +
520G TYR* 3.6 16.7 - - - -
71H ARG 2.9 24.5 + - - -
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Residues in contact with LYS 519 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508G ILE* 3.6 2.3 - - - -
509G THR* 2.7 39.7 + - + +
510G GLY* 2.9 29.1 + - - +
511G TRP 4.0 13.5 + - - +
512G ASN* 4.0 36.6 + - + +
518G SER* 1.3 75.0 - - - +
520G TYR* 1.3 57.1 + - - +
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Residues in contact with TYR 520 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G SER* 4.6 0.9 + - - -
483G GLN* 3.3 33.7 + - - +
484G PRO* 2.6 38.4 + - + +
485G ALA 5.2 0.2 - - - -
506G ARG* 3.3 58.1 - - + +
507G LYS* 3.2 21.3 - - - -
508G ILE* 3.5 11.9 - - + -
509G THR* 4.0 1.4 - - - +
518G SER* 3.6 22.6 + - - -
519G LYS* 1.3 77.2 - - - +
521G ASP* 1.3 72.3 + - - +
522G ASN* 4.9 1.8 - - - +
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Residues in contact with ASP 521 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G SER* 3.0 15.9 + - - +
13G ASN* 4.6 21.1 + - - +
115G THR* 5.0 4.7 - - - +
505G GLU* 3.5 1.4 - - - +
506G ARG* 3.2 7.1 - - - -
507G LYS* 3.0 45.6 + - + +
509G THR* 3.1 30.9 + - + +
520G TYR* 1.3 80.2 - - - +
522G ASN* 1.3 68.4 + - - +
523G LYS* 5.5 2.2 - - + -
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Residues in contact with ASN 522 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G PHE* 4.4 3.4 - - + +
11G THR* 3.4 0.9 - - - -
12G SER* 2.9 41.8 + - - +
504G TYR* 3.3 28.8 + - + +
505G GLU 3.4 4.0 - - - +
506G ARG* 3.7 19.2 + - - +
520G TYR* 4.9 1.4 - - - +
521G ASP* 1.3 82.2 + - - +
523G LYS* 1.3 71.6 + - - +
524G ILE* 6.1 2.2 - - + -
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Residues in contact with LYS 523 (chain G).
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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9G LYS* 4.2 28.0 - - + +
10G PHE 3.3 5.8 - - - +
11G THR* 3.8 17.5 - - + -
13G ASN* 5.7 0.4 - - - +
118G THR* 4.2 26.3 + - - +
503G GLY 3.8 0.7 - - - +
504G TYR* 3.3 5.6 - - - -
505G GLU* 2.8 70.4 + - + +
507G LYS* 4.7 16.7 - - - +
521G ASP* 5.5 2.5 - - + -
522G ASN* 1.3 84.8 - - - +
524G ILE* 1.3 62.0 + - - +
547G SER 5.5 3.6 + - - -
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Residues in contact with ILE 524 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G LYS* 3.5 2.8 - - - +
10G PHE* 2.9 54.9 + - + +
502G LEU* 4.4 16.2 - - + -
503G GLY 3.2 11.9 - - - +
504G TYR* 4.0 21.3 - - + -
522G ASN* 5.9 1.6 - - + -
523G LYS* 1.3 76.7 - - - +
525G GLY* 1.3 59.9 + - - +
526G PHE* 5.4 4.3 - - + -
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Residues in contact with GLY 525 (chain G).
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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8G ALA 3.4 11.7 - - - -
9G LYS* 3.6 10.5 - - - +
501G ASN 3.9 0.5 - - - +
502G LEU* 3.6 2.1 - - - +
503G GLY* 3.1 28.8 + - - -
524G ILE* 1.3 75.0 - - - +
526G PHE* 1.3 75.5 + - - -
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Residues in contact with PHE 526 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ASN* 3.3 3.8 - - - +
8G ALA* 2.9 42.5 + - + +
501G ASN 3.5 5.4 - - - +
502G LEU* 3.2 39.5 - - + -
524G ILE* 5.4 4.9 - - + -
525G GLY* 1.3 86.4 - - - -
527G ASN* 1.3 61.8 + - - +
528G ILE* 6.4 0.4 - - + -
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Residues in contact with ASN 527 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ASN* 3.4 25.0 - - + +
500G VAL* 3.9 2.4 - - - +
501G ASN* 2.9 54.8 + - - +
526G PHE* 1.3 77.2 - - - +
528G ILE* 1.3 71.2 + - - +
529G GLU* 4.6 7.0 + - + +
543G GLN* 5.4 7.0 + - - +
544G MET* 6.0 2.8 - - - +
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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