Contacts of the helix formed by residues 400 - 413 (chain A) in PDB entry 3RC3
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 PRO 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A SER 3.5 4.2 - - - +
399A LEU* 1.3 89.8 - - + +
401A PRO* 1.3 79.0 - - + +
402A GLY 3.3 0.6 + - - -
403A THR* 3.3 3.9 + - - +
404A LYS* 3.0 18.9 + - - +
629A GLU* 4.6 3.6 - - + -
632A HIS* 3.4 27.8 - - + +
663A ASP* 3.5 24.0 - - - +
666A ILE* 3.7 46.7 - - + -
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Residues in contact with PRO 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS* 5.3 17.7 - - + +
235A LEU* 4.0 22.9 - - + -
238A HIS* 6.3 2.5 - - + -
399A LEU 4.3 1.3 - - - +
400A PRO* 1.3 92.0 - - + +
402A GLY* 1.3 63.7 + - - +
404A LYS* 3.3 10.3 + - + +
405A LEU* 3.0 31.3 + - + +
632A HIS* 4.1 14.4 - - + +
663A ASP* 3.9 3.6 - - - +
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Residues in contact with GLY 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A PRO* 1.3 74.3 - - - +
403A THR* 1.3 55.9 + - - +
405A LEU* 3.5 10.0 + - - +
406A ALA* 2.9 29.3 + - - +
663A ASP* 2.8 27.3 + - - -
667A GLN* 4.2 8.7 + - - -
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Residues in contact with THR 403 (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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399A LEU* 4.0 12.3 - - + -
400A PRO* 3.3 13.4 + - - +
402A GLY* 1.3 73.8 - - - +
404A LYS* 1.4 66.7 + - - +
406A ALA* 3.1 5.5 + - - +
407A GLN* 2.9 26.0 + - + +
663A ASP* 3.0 16.9 + - - -
666A ILE* 3.9 4.5 - - - +
667A GLN* 3.2 29.0 + - + +
670A VAL* 3.7 42.6 - - + -
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Residues in contact with LYS 404 (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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235A LEU* 3.9 28.3 - - + +
395A ILE* 4.0 13.4 - - + +
396A TYR 3.4 15.5 - - - +
397A GLY* 2.8 30.0 + - - -
399A LEU* 3.2 39.5 + - + +
400A PRO 3.0 11.3 + - - +
401A PRO* 3.3 9.8 + - + +
403A THR* 1.4 77.5 - - - +
405A LEU* 1.3 58.5 + - + +
407A GLN* 3.5 3.2 + - - +
408A ALA* 2.9 29.7 + - - +
426A ALA* 5.7 2.7 - - - +
431A LEU* 4.5 19.4 - - + +
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Residues in contact with LEU 405 (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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235A LEU* 4.1 17.0 - - + -
242A GLU* 5.8 3.6 - - - +
401A PRO* 3.0 24.4 + - + +
402A GLY* 3.7 8.3 - - - +
404A LYS* 1.3 78.6 - - - +
406A ALA* 1.3 57.1 + - - +
408A ALA* 3.6 4.6 - - + +
409A LYS* 2.9 30.7 + - - +
431A LEU* 3.9 22.0 - - + -
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Residues in contact with ALA 406 (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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402A GLY 2.9 18.4 + - - +
403A THR 3.1 4.2 + - - +
405A LEU* 1.3 72.7 - - - +
407A GLN* 1.3 70.7 + - + +
409A LYS* 3.3 7.1 + - - +
410A LYS* 3.0 30.4 + - + +
667A GLN* 3.4 35.4 - - + +
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Residues in contact with GLN 407 (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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392A SER 4.6 0.3 - - - +
393A ALA* 3.3 16.6 - - - +
394A VAL* 2.8 47.3 + - - +
395A ILE* 4.0 6.7 - - + -
399A LEU* 5.0 0.4 - - + -
403A THR* 2.9 21.5 + - + +
404A LYS 3.9 2.7 - - - +
406A ALA* 1.3 80.6 - - + +
408A ALA* 1.4 62.1 + - - +
410A LYS* 3.3 8.3 + - - +
411A PHE* 3.0 22.5 + - - +
667A GLN* 5.0 3.2 + - - +
670A VAL* 3.9 22.2 - - + +
671A HIS* 3.9 18.2 - - - +
902A AZI 3.3 25.2 + - - -
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Residues in contact with ALA 408 (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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395A ILE* 3.9 12.0 - - + +
404A LYS 2.9 19.2 + - - +
405A LEU* 3.6 9.4 - - + +
406A ALA 3.3 0.2 - - - -
407A GLN* 1.4 78.1 - - - +
409A LYS* 1.3 51.6 + - - +
411A PHE* 3.3 3.9 + - - +
412A ASN* 2.7 45.4 + - - +
431A LEU* 4.5 9.9 - - + -
432A ASN 5.0 1.8 - - - +
433A LEU* 3.7 23.6 - - + -
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Residues in contact with LYS 409 (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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405A LEU 2.9 17.9 + - - +
406A ALA* 3.7 7.4 - - - +
407A GLN 3.3 0.2 - - - -
408A ALA* 1.3 76.5 - - - +
410A LYS* 1.3 57.0 + - + +
412A ASN* 3.7 7.2 - - + +
413A ASP* 2.9 37.3 + - + +
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Residues in contact with LYS 410 (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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391A GLU* 4.7 5.9 + - - -
393A ALA* 5.3 0.4 - - + -
406A ALA* 3.0 23.3 + - + +
407A GLN* 3.8 10.1 - - - +
409A LYS* 1.3 75.9 - - - +
411A PHE* 1.3 63.7 + - - +
413A ASP* 3.4 4.6 + - - -
416A ASP* 3.0 44.5 + - - +
418A CYS* 3.4 15.8 - - + +
419A LYS* 3.0 15.4 + - - -
671A HIS* 3.9 20.7 - - + +
902A AZI 3.3 31.6 - - - +
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Residues in contact with PHE 411 (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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367A GLY* 3.9 15.3 - - - -
368A ASP 3.4 11.9 - - - -
369A CYS* 4.8 0.2 - - + -
393A ALA* 3.8 14.9 - - + +
407A GLN 3.0 16.7 + - - +
408A ALA* 3.7 2.7 - - - +
410A LYS* 1.3 76.6 - - - +
412A ASN* 1.3 70.8 + - - +
418A CYS 3.8 6.3 - - - -
419A LYS* 2.9 50.3 + - - -
420A ILE 3.5 18.2 - - - -
421A LEU* 3.4 35.7 - - + -
433A LEU* 4.4 4.9 - - + -
434A SER 3.2 27.5 - - - +
435A ILE* 3.7 20.2 - - + -
477A ARG* 4.8 1.7 + - - -
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Residues in contact with ASN 412 (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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408A ALA* 2.7 29.5 + - - +
409A LYS* 3.9 6.7 - - - +
411A PHE* 1.3 82.5 - - - +
413A ASP* 1.3 61.4 + - - +
414A PRO* 3.1 3.5 - - - +
432A ASN* 2.9 26.5 + - - +
433A LEU* 3.4 5.9 - - - +
434A SER* 2.8 39.6 + - - +
477A ARG* 2.9 26.4 + - - +
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Residues in contact with ASP 413 (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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409A LYS* 2.9 22.1 + - + +
410A LYS* 3.8 6.5 - - - +
411A PHE 3.3 0.8 - - - -
412A ASN* 1.3 74.2 - - - +
414A PRO* 1.3 68.2 - - - +
415A ASN* 2.8 23.7 + - - +
416A ASP* 3.2 24.9 + - + +
419A LYS* 2.6 27.8 + - - -
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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