Contacts of the helix formed by residues 431 - 448 (chain C) in PDB entry 5W5G
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 THR 431 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C GLU* 2.6 33.8 + - - +
383C ARG 3.6 27.8 - - - +
384C MET* 3.8 19.3 - - - +
387C VAL* 4.1 5.4 - - + -
388C PHE* 4.7 0.9 - - + -
409C ASN* 3.3 22.7 - - - +
411C PRO* 4.9 2.2 - - - -
430C ILE* 1.3 76.3 - - - +
432C VAL* 1.3 65.1 + - - +
433C PHE 3.3 1.7 + - - -
434C GLY 3.0 14.2 + - - -
435C CYS* 3.1 23.1 + - - -
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Residues in contact with VAL 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C ARG* 4.6 2.5 - - - +
408C LEU 3.4 24.0 - - - +
409C ASN* 2.9 18.8 + - - +
410C MET 3.4 22.2 - - - +
411C PRO* 3.8 12.0 - - + -
412C HIS* 5.9 3.1 - - + -
431C THR* 1.3 70.8 - - - +
433C PHE* 1.3 68.6 + - + +
435C CYS* 3.3 12.1 + - + +
436C MET* 3.2 23.3 + - + +
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Residues in contact with PHE 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C GLU* 3.9 14.8 - - - +
408C LEU 5.6 1.8 - - - -
409C ASN* 2.9 28.9 + - + +
431C THR 3.2 0.2 - - - -
432C VAL* 1.3 86.6 - - + +
434C GLY* 1.3 59.6 + - - +
436C MET* 3.7 12.9 - - + +
437C GLN* 2.8 39.7 + - + +
623C HIS* 5.0 17.5 - + + +
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Residues in contact with GLY 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C GLY* 4.3 2.3 - - - -
382C GLU* 3.8 18.1 - - - +
430C ILE* 3.8 9.0 - - - +
431C THR* 3.0 16.3 + - - -
433C PHE* 1.3 74.9 - - - +
435C CYS* 1.3 63.3 + - - +
437C GLN* 3.3 18.1 + - - +
438C ALA* 3.1 24.8 + - - +
597C LEU* 4.5 2.3 - - - +
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Residues in contact with CYS 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C PRO* 6.1 4.5 - - - -
430C ILE* 3.5 19.2 - - - +
431C THR 3.1 18.1 + - - -
432C VAL* 3.4 12.6 - - + +
434C GLY* 1.3 75.9 - - - +
436C MET* 1.3 55.4 + - - +
438C ALA* 3.6 2.8 + - - +
439C ARG* 2.9 28.5 + - - +
465C GLN* 5.9 1.8 - - - -
469C ASN* 3.4 35.4 - - - +
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Residues in contact with MET 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C VAL* 3.2 12.0 + - + +
433C PHE* 3.7 17.3 - - + +
434C GLY 3.2 0.4 - - - -
435C CYS* 1.3 77.1 - - - +
437C GLN* 1.3 65.9 + - - +
439C ARG* 3.1 24.4 + - - -
440C LEU* 2.9 56.7 + - + +
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Residues in contact with GLN 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C GLY* 3.4 8.0 - - - -
382C GLU* 3.0 41.6 + - - +
433C PHE* 2.8 29.4 + - + +
434C GLY* 3.5 4.6 - - - +
436C MET* 1.3 73.2 - - - +
438C ALA* 1.3 62.6 + - - +
440C LEU* 3.4 4.7 + - - +
441C VAL* 3.3 24.9 + - - +
596C TYR* 3.6 21.5 - - - +
597C LEU* 3.7 9.6 - - + -
621C LEU* 3.8 26.9 - - + +
623C HIS* 3.3 30.8 + - + +
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Residues in contact with ALA 438 (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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434C GLY 3.1 14.1 + - - +
435C CYS* 3.6 5.4 - - - +
437C GLN* 1.3 81.4 - - - +
439C ARG* 1.3 61.5 + - - +
441C VAL* 3.2 2.3 + - - +
442C GLY 3.1 18.0 + - - -
466C THR* 3.6 41.1 - - + +
469C ASN* 3.8 8.7 - - + -
470C ILE* 3.5 11.6 - - + +
597C LEU* 3.8 12.7 - - + +
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Residues in contact with ARG 439 (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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435C CYS 2.9 18.8 + - - +
436C MET* 3.1 31.8 + - - +
438C ALA* 1.3 76.6 - - - +
440C LEU* 1.3 58.0 + - - +
442C GLY 3.3 1.2 + - - -
443C GLU* 2.9 53.6 + - - +
469C ASN* 3.6 14.8 + - + +
472C LYS* 5.0 5.2 - - + -
473C GLY* 3.6 16.0 - - - +
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Residues in contact with LEU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C MET* 2.9 44.1 + - + +
437C GLN* 3.8 5.2 - - - +
439C ARG* 1.3 72.5 - - - +
441C VAL* 1.3 61.4 + - + +
443C GLU* 3.4 21.3 + - - +
444C ALA* 2.8 28.8 + - - +
621C LEU* 4.5 26.2 - - + -
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Residues in contact with VAL 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C GLN 3.3 12.3 + - - +
438C ALA 3.2 9.5 + - - +
440C LEU* 1.3 78.6 - - - +
442C GLY* 1.3 58.1 + - - +
444C ALA* 3.1 9.3 + - - +
445C LEU* 3.0 32.8 + - + +
470C ILE* 4.6 12.1 - - + -
597C LEU* 4.0 32.1 - - + +
599C PHE* 4.1 19.5 - - + -
618C ILE* 3.9 23.5 - - + +
621C LEU* 5.0 11.2 - - + -
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Residues in contact with GLY 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C ALA 3.1 8.1 + - - -
439C ARG 3.7 2.5 - - - -
441C VAL* 1.3 78.3 - - - +
443C GLU* 1.3 60.2 + - - +
445C LEU* 3.3 7.8 + - - +
446C LEU 3.1 17.7 + - - -
470C ILE* 3.3 33.8 - - - +
473C GLY 3.5 12.3 - - - +
474C LEU* 3.5 7.7 - - - -
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Residues in contact with GLU 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C ARG* 2.9 44.0 + - - +
440C LEU* 3.6 20.9 - - - +
442C GLY* 1.3 75.3 - - - +
444C ALA* 1.3 58.9 + - - +
446C LEU* 3.2 7.1 + - + +
447C GLU* 2.9 46.9 + - - +
473C GLY* 3.4 20.7 + - - +
475C GLN* 5.6 3.6 - - - +
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Residues in contact with ALA 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C LEU 2.8 18.0 + - - +
441C VAL* 3.1 7.4 + - - +
443C GLU* 1.3 75.2 - - - +
445C LEU* 1.3 56.8 + - - +
447C GLU* 3.5 16.9 + - - +
448C SER* 3.1 27.0 + - - -
618C ILE* 3.3 29.2 - - + +
619C LEU* 5.4 3.6 - - + +
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Residues in contact with LEU 445 (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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376C PHE* 5.5 0.4 - - + -
441C VAL* 3.0 18.8 + - + +
442C GLY* 3.6 9.2 - - - +
443C GLU 3.2 0.2 - - - -
444C ALA* 1.3 75.0 - - - +
446C LEU* 1.3 62.0 + - - +
448C SER* 2.9 16.0 + - - -
450C THR* 3.0 36.3 + - + +
452C ILE* 4.2 16.8 - - + -
470C ILE* 4.5 9.0 - - + -
474C LEU* 3.9 29.6 - - + -
561C LEU* 4.6 2.9 - - + -
599C PHE* 4.1 31.0 - - + -
617C PRO* 4.1 13.5 - - + -
618C ILE* 3.7 19.1 - - + -
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Residues in contact with LEU 446 (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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442C GLY 3.1 13.1 + - - +
443C GLU* 3.5 9.9 - - + +
445C LEU* 1.3 76.8 - - - +
447C GLU* 1.3 58.2 - - + +
449C ASN* 3.0 28.2 + - - +
450C THR 5.2 0.7 - - - -
473C GLY 4.2 7.6 - - - +
474C LEU* 3.6 25.9 - - + +
475C GLN* 3.2 36.3 - - + +
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Residues in contact with GLU 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C GLU* 2.9 38.1 + - - +
444C ALA* 3.7 14.3 - - - +
445C LEU 3.3 0.2 - - - -
446C LEU* 1.3 78.2 - - + +
448C SER* 1.3 59.7 + - - +
449C ASN* 3.2 9.9 + - - +
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Residues in contact with SER 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ALA 3.1 14.8 + - - -
445C LEU* 2.9 13.7 + - - -
447C GLU* 1.3 73.9 - - - +
449C ASN* 1.3 69.6 + - - +
450C THR* 2.6 26.4 + - - -
617C PRO* 3.7 23.4 + - - -
618C ILE* 4.3 2.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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