Contacts of the helix formed by residues 399 - 414 (chain A) in PDB entry 1RQG
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 399 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A GLU 3.9 3.6 + - - +
395A GLU* 3.0 22.4 + - - +
397A VAL 3.1 0.4 + - - -
398A ASN* 1.3 79.4 - - - +
400A LEU* 1.3 74.8 + - - +
401A GLY 3.4 0.4 - - - -
402A ASN* 3.3 0.6 + - - +
403A PHE* 2.9 21.5 + - - +
460A MET* 3.6 11.0 - - + +
463A ALA* 3.3 21.5 - - - +
464A SER* 3.5 26.2 + - - +
467A ASN* 3.0 30.6 + - - +
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Residues in contact with LEU 400 (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 GLU 3.3 4.2 + - - -
396A LEU* 3.8 16.2 - - + +
399A ASN* 1.3 85.0 + - - +
401A GLY* 1.3 63.6 + - - +
403A PHE* 3.4 1.4 + - - +
404A VAL* 3.1 35.1 + - + +
459A VAL* 5.9 0.2 - - + -
460A MET* 3.7 20.9 - - + -
463A ALA* 3.6 9.2 - - + -
500A LEU* 3.3 40.4 - - + -
504A LEU* 3.2 37.9 - - + -
508A LEU* 5.4 0.9 - - + -
544A LEU* 5.0 0.7 - - + -
545A PHE* 4.1 19.3 - - + -
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Residues in contact with GLY 401 (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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396A LEU 2.9 21.2 + - - -
397A VAL* 3.6 4.0 - - - -
400A LEU* 1.3 74.2 - - - +
402A ASN* 1.3 63.1 + - - +
404A VAL* 3.6 1.9 + - - +
405A HIS* 3.0 24.8 + - - +
543A ILE* 5.9 1.6 - - - +
544A LEU* 4.0 16.6 + - - +
545A PHE* 3.8 17.9 - - - -
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Residues in contact with ASN 402 (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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397A VAL 2.9 8.8 + - - +
398A ASN* 2.8 40.0 + - - +
399A ASN 3.5 1.6 - - - +
400A LEU 3.2 0.4 - - - -
401A GLY* 1.3 74.6 - - - +
403A PHE* 1.3 63.5 + - - +
405A HIS* 3.2 6.7 + - - +
406A ARG* 2.9 45.0 + - - +
467A ASN* 4.6 4.5 - - - +
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Residues in contact with PHE 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 ASN 2.9 20.7 + - - +
400A LEU* 3.6 3.8 - - - +
402A ASN* 1.3 71.8 - - - +
404A VAL* 1.3 72.9 + - + +
406A ARG* 3.0 8.8 + - - +
407A ALA* 2.9 23.8 + - + +
463A ALA 4.3 7.4 - - - +
466A GLY* 3.5 34.3 - - - -
467A ASN* 3.5 20.1 + - - +
469A TYR* 6.0 0.2 - + - -
470A PHE* 4.1 21.8 - + - -
493A SER* 3.5 23.1 - - - -
496A ILE* 3.7 29.8 - - + -
497A VAL* 3.4 22.2 - - + -
500A LEU* 3.9 21.8 - - + -
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Residues in contact with VAL 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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400A LEU* 3.1 25.0 + - + +
401A GLY 3.8 1.1 - - - +
403A PHE* 1.3 88.9 - - + +
405A HIS* 1.3 64.3 + - - +
407A ALA* 3.5 2.1 + - - +
408A LEU* 3.2 40.7 + - + +
497A VAL* 4.3 20.2 - - + -
500A LEU* 4.8 1.6 - - + -
515A ILE* 4.0 19.5 - - + -
518A LEU* 4.3 6.3 - - + -
544A LEU* 3.5 37.5 - - + -
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Residues in contact with HIS 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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401A GLY 3.0 19.2 + - - +
402A ASN* 3.5 5.4 - - - +
403A PHE 3.1 0.2 - - - -
404A VAL* 1.3 77.2 - - - +
406A ARG* 1.3 65.0 + - + +
408A LEU* 3.9 3.7 - - + +
409A THR* 2.7 52.5 + - + -
541A PRO* 4.2 12.6 + - + +
542A GLU 3.0 28.3 + - - +
543A ILE* 4.5 20.4 - - + +
544A LEU 5.8 1.1 - - - +
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Residues in contact with ARG 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 ASN* 2.9 30.8 + - - +
403A PHE* 3.4 6.3 - - - +
405A HIS* 1.3 79.3 - - + +
407A ALA* 1.3 65.3 + - - +
409A THR* 3.1 7.3 + - - -
410A PHE* 3.0 42.8 + - + -
467A ASN* 2.8 59.6 + - - +
470A PHE* 3.6 27.3 - - + +
471A ASP* 2.9 24.5 + - - +
476A TRP* 4.6 10.3 - - - -
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Residues in contact with ALA 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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403A PHE* 2.9 14.6 + - + +
404A VAL 3.5 8.7 - - - +
406A ARG* 1.3 74.6 - - - +
408A LEU* 1.3 63.4 + - + +
410A PHE* 3.0 13.5 + - - +
411A VAL* 3.1 14.2 + - - +
470A PHE* 4.1 23.6 - - + -
490A VAL* 5.4 0.9 - - - +
493A SER* 4.4 5.6 + - - +
494A LEU* 4.1 15.4 - - + +
497A VAL* 3.9 22.7 - - + -
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Residues in contact with LEU 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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404A VAL* 3.2 24.0 + - + +
405A HIS* 4.0 3.8 - - - +
407A ALA* 1.3 79.0 - - + +
409A THR* 1.3 65.3 + - - +
410A PHE 2.8 1.7 + - - -
411A VAL* 3.0 9.2 - - + +
412A ASN* 2.9 24.4 + - - +
494A LEU* 4.7 4.5 - - + -
497A VAL* 5.6 2.0 - - + -
518A LEU* 3.6 50.3 - - + +
519A LEU* 4.3 16.6 - - + -
538A VAL* 3.3 33.2 - - + -
539A ARG 4.3 2.7 - - - +
541A PRO* 3.7 17.5 - - + -
542A GLU 5.0 1.8 - - - +
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Residues in contact with THR 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 HIS* 2.7 53.3 + - + -
406A ARG* 3.3 8.3 - - - -
408A LEU* 1.3 72.2 - - - +
410A PHE* 1.3 63.5 + - + +
412A ASN* 4.0 1.9 - - - +
413A ARG* 3.3 45.4 + - - +
541A PRO* 3.4 17.9 - - + +
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Residues in contact with PHE 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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406A ARG* 3.0 31.5 + - + -
407A ALA 3.5 5.6 - - - +
408A LEU 2.8 2.0 + - - -
409A THR* 1.3 85.2 - - + +
411A VAL* 1.3 63.3 + - - +
412A ASN 2.8 6.7 + - - -
413A ARG* 2.9 18.0 + - - +
414A TYR* 3.0 46.2 + + + +
415A PHE* 4.6 0.2 - - - -
470A PHE* 3.0 42.8 - + + -
475A PRO* 4.7 6.3 - - + -
476A TRP* 4.0 36.6 - + + -
490A VAL* 4.7 12.1 - - + -
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Residues in contact with VAL 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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407A ALA 3.1 7.5 + - - +
408A LEU* 3.0 28.0 - - - +
410A PHE* 1.3 76.4 - - - +
412A ASN* 1.3 51.2 + - - +
415A PHE* 3.4 19.1 + - + +
417A GLY* 2.7 25.5 + - - -
418A VAL 3.8 29.8 - - - +
419A VAL 4.5 0.2 - - - +
420A PRO* 4.3 0.7 - - + -
490A VAL* 3.8 23.0 - - + +
494A LEU* 3.7 27.4 - - + -
538A VAL* 4.1 20.9 - - + -
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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 LEU 2.9 15.7 + - - +
409A THR 4.2 2.0 - - - +
410A PHE 2.8 0.8 - - - -
411A VAL* 1.3 79.2 - - - +
413A ARG* 1.3 62.6 + - - +
416A ASP* 3.5 21.8 + - - +
417A GLY* 3.3 19.7 - - - +
538A VAL* 4.3 2.1 - - - +
539A ARG 3.0 25.1 - - - +
540A LYS* 3.7 19.5 - - - +
541A PRO* 3.5 24.8 - - + +
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Residues in contact with ARG 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 THR* 3.3 34.9 + - - +
410A PHE* 2.9 8.0 + - - -
412A ASN* 1.3 81.0 - - - +
414A TYR* 1.3 95.9 + - + +
415A PHE 4.0 0.2 + - - -
416A ASP* 4.9 2.8 + - - +
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Residues in contact with TYR 414 (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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410A PHE* 3.0 31.0 + + + +
413A ARG* 1.3 112.5 - - + +
415A PHE* 1.3 87.6 + - + +
416A ASP 3.8 0.7 - - - -
475A PRO 5.4 0.7 - - - -
476A TRP* 3.9 22.7 + - - +
479A ALA* 3.0 39.0 - - + -
480A LYS* 3.9 21.0 + - - -
486A THR* 5.1 6.1 - - + -
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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