Contacts of the helix formed by residues 520 - 532 (chain C) in PDB entry 1CX2
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 GLU 520 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C THR* 5.3 0.5 - - - +
86C PRO* 3.7 20.8 - - + +
87C ASN* 4.1 17.3 + - - +
467C ARG* 2.7 43.9 + - - +
472C LEU* 3.8 8.6 - - + +
473C LYS 5.0 0.2 + - - -
475C TYR* 3.1 12.6 + - - -
510C GLU* 3.8 3.2 + - - +
511C LYS 4.6 1.6 + - - -
513C ARG* 3.8 30.9 - - + +
519C GLY* 1.3 70.0 - - - -
521C THR* 1.3 54.0 + - - +
523C VAL* 3.0 1.4 + - - -
524C GLU* 2.7 52.6 + - + +
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Residues in contact with THR 521 (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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463C LEU* 4.0 24.9 - - + -
466C TYR* 6.4 0.2 - - + -
467C ARG* 2.5 41.1 + - + +
472C LEU* 4.1 6.1 - - + -
475C TYR* 3.7 3.5 + - - -
503C LEU* 4.5 7.9 - - + -
507C LEU* 3.9 17.0 - - + +
510C GLU* 3.0 23.1 + - - -
520C GLU* 1.3 78.4 - - - +
522C MET* 1.3 64.6 + - - +
525C LEU* 3.3 26.9 + - + +
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Residues in contact with MET 522 (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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384C LEU* 3.3 35.2 - - + +
387C TRP* 2.9 35.4 - - + +
434C VAL* 3.6 22.7 - - + -
507C LEU* 3.2 33.6 - - + +
508C LEU* 4.8 6.5 - - + -
510C GLU* 3.8 3.0 + - - +
518C PHE* 3.5 32.5 - - + -
519C GLY 3.3 9.5 + - - +
520C GLU 3.2 0.2 - - - -
521C THR* 1.3 80.7 - - - +
523C VAL* 1.3 66.0 + - - +
524C GLU 3.2 0.3 + - - -
525C LEU* 4.3 1.0 - - - +
526C GLY* 3.2 20.3 + - - -
701C S58 4.5 2.9 - - + -
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Residues in contact with VAL 523 (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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355C TYR* 5.5 0.7 - - - +
513C ARG* 3.2 28.5 - - - +
518C PHE* 3.3 37.5 - - + +
519C GLY 3.0 13.5 + - - +
520C GLU 3.7 1.6 - - - +
522C MET* 1.3 80.5 - - - +
524C GLU* 1.3 63.0 + - - +
527C ALA* 3.2 29.8 + - + +
701C S58 3.5 45.8 - - + +
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Residues in contact with GLU 524 (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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86C PRO* 3.7 20.0 - - + +
120C ARG* 5.1 14.7 + - - -
470C PHE* 3.6 13.4 - - - +
472C LEU* 3.4 38.2 - - + +
513C ARG* 3.7 16.1 + - - +
520C GLU* 2.7 29.9 + - + +
522C MET 3.2 0.2 + - - -
523C VAL* 1.3 83.1 - - - +
525C LEU* 1.3 61.0 + - - +
527C ALA* 5.1 2.1 - - - +
528C PRO* 3.0 27.0 - - - +
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Residues in contact with LEU 525 (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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380C GLU* 5.2 4.3 - - + -
384C LEU* 3.6 21.8 - - + -
466C TYR* 3.9 30.3 - - + +
467C ARG* 4.9 0.4 - - - +
470C PHE* 3.2 46.3 - - + -
472C LEU* 4.6 7.4 - - + -
503C LEU* 3.4 36.8 - - + -
507C LEU* 5.7 0.4 - - + -
521C THR* 3.3 21.0 + - + +
524C GLU* 1.3 79.3 - - - +
526C GLY* 1.3 61.4 + - - +
528C PRO* 3.4 7.3 - - - +
529C PHE* 3.4 25.7 - - + -
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Residues in contact with GLY 526 (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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381C PHE* 3.4 15.0 - - - -
384C LEU* 4.0 6.9 - - - +
522C MET 3.2 9.8 + - - -
525C LEU* 1.3 79.7 - - - +
527C ALA* 1.3 58.8 + - - +
528C PRO 3.3 0.2 - - - -
529C PHE 3.3 0.3 + - - -
530C SER* 2.8 33.8 + - - -
701C S58 3.4 20.2 - - - -
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Residues in contact with ALA 527 (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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120C ARG* 3.3 29.6 - - - +
523C VAL* 3.2 22.3 + - + +
524C GLU* 4.8 3.1 - - - +
526C GLY* 1.3 73.8 - - - +
528C PRO* 1.3 72.4 - - + +
530C SER* 3.1 1.7 + - - -
531C LEU* 3.1 26.7 + - - +
701C S58 3.3 28.7 - - + -
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Residues in contact with PRO 528 (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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120C ARG* 3.3 33.0 - - + +
121C SER* 3.3 18.9 + - - +
123C LEU* 4.3 5.6 - - + -
124C ILE* 3.5 21.2 - - + +
470C PHE* 4.3 12.8 - - + -
524C GLU* 3.0 25.4 - - - +
525C LEU 3.4 8.5 - - - +
527C ALA* 1.3 95.6 - - + +
529C PHE* 1.3 65.7 + - + +
531C LEU 3.4 4.5 + - - -
532C LYS* 3.5 5.0 + - - +
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Residues in contact with PHE 529 (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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123C LEU 4.9 2.0 - - - -
124C ILE* 4.0 22.7 - - + -
151C ALA* 3.4 20.4 - - + -
375C ASN* 4.9 2.9 - - - +
378C ALA* 4.2 11.4 - - + -
380C GLU* 3.8 26.7 - - + -
381C PHE* 2.9 53.3 - + + -
384C LEU* 4.9 2.5 - - + -
470C PHE* 3.2 37.2 - + - -
525C LEU* 3.4 15.7 - - + +
526C GLY 3.3 2.4 + - - +
527C ALA 3.3 0.2 - - - -
528C PRO* 1.3 84.8 - - - +
530C SER* 1.3 57.7 + - - +
531C LEU 3.4 1.0 + - - -
532C LYS* 3.8 3.1 + - - +
533C GLY* 3.6 15.8 + - - -
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Residues in contact with SER 530 (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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205C PHE* 5.3 5.4 - - - -
209C PHE* 5.9 1.4 - - - -
344C VAL* 5.6 1.2 - - - +
348C TYR* 5.8 1.0 - - - -
349C VAL* 5.5 4.1 - - - +
381C PHE* 3.4 21.3 - - - -
385C TYR* 4.3 6.9 + - - -
526C GLY 2.8 21.6 + - - -
527C ALA 3.1 3.1 + - - -
529C PHE* 1.3 73.2 - - - +
531C LEU* 1.3 59.5 + - - +
533C GLY* 4.2 1.3 - - - -
534C LEU* 2.9 43.2 - - - +
701C S58 4.1 22.2 - - - -
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Residues in contact with LEU 531 (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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116C VAL 4.4 1.6 - - - +
117C LEU* 4.0 29.8 - - + +
120C ARG* 3.8 24.7 - - + -
121C SER* 3.9 9.9 - - - +
345C ILE* 3.8 28.0 - - + -
349C VAL* 5.2 2.7 - - + -
371C PHE* 6.0 0.2 - - - -
527C ALA 3.1 14.1 + - - +
529C PHE 3.3 0.6 - - - -
530C SER* 1.3 78.3 - - - +
532C LYS* 1.3 55.7 + - - +
533C GLY 3.1 5.2 - - - -
534C LEU* 3.1 6.8 + - + +
535C MET* 2.7 40.5 + - + +
701C S58 3.1 42.2 - - + -
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Residues in contact with LYS 532 (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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121C SER* 3.7 25.8 - - - +
124C ILE* 3.8 32.8 - - + +
126C SER* 3.7 19.1 - - - -
371C PHE* 3.6 21.5 - - + -
372C GLN* 2.7 38.6 + - - +
374C GLN 3.4 17.9 + - - +
375C ASN* 3.5 21.7 - - - +
528C PRO 3.5 9.4 + - - +
529C PHE* 4.5 2.7 - - - +
531C LEU* 1.3 77.6 - - - +
533C GLY* 1.3 58.1 + - - +
536C GLY* 3.2 27.1 + - - +
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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