Contacts of the helix formed by residues 443 - 459 (chain A) in PDB entry 1N54
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 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403A ASP* 5.9 0.2 - - - -
439A GLN* 3.9 21.9 + - - +
440A ASP* 2.9 32.3 + - - +
441A PRO 3.7 0.2 - - - +
442A GLU* 1.3 78.6 - - - +
444A PRO* 1.3 75.3 - - - +
445A LYS 3.6 0.2 - - - -
446A PRO* 3.1 6.3 - - - +
447A LYS* 3.0 21.9 + - - +
738A PRO* 5.1 6.7 - - - +
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Residues in contact with PRO 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LEU* 4.3 13.0 - - + +
403A ASP* 4.2 41.1 - - + +
410A VAL* 6.5 1.3 - - + -
442A GLU 3.8 3.8 - - - +
443A SER* 1.3 84.0 - - - +
445A LYS* 1.3 68.8 + - - +
447A LYS* 3.0 11.0 + - + +
448A PHE* 2.8 25.7 + - - +
738A PRO* 5.6 5.6 - - + -
741A LYS* 4.9 15.9 - - + -
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Residues in contact with LYS 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A TYR* 3.6 33.0 - - + +
400A MET* 3.8 31.0 + - - +
402A LEU* 4.3 20.8 - - + +
403A ASP* 3.2 35.1 + - - +
435A ASP* 3.4 16.7 + - - +
436A CYS* 4.2 2.9 - - + -
439A GLN* 3.7 21.2 + - - +
444A PRO* 1.3 81.0 - - - +
446A PRO* 1.4 74.4 - - + +
448A PHE* 2.9 16.6 + - - +
449A VAL* 3.4 8.0 + - - +
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Residues in contact with PRO 446 (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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436A CYS* 3.7 32.7 - - + +
439A GLN* 3.2 30.5 - - + +
440A ASP 3.2 22.2 - - - +
441A PRO* 4.3 2.9 - - + +
443A SER 3.1 23.3 - - - +
445A LYS* 1.4 82.4 - - + +
447A LYS* 1.3 59.3 + - - +
448A PHE 3.1 0.2 + - - -
449A VAL* 3.2 4.6 + - + +
450A ARG* 3.0 27.4 + - - +
476A LEU* 3.8 18.2 - - + +
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Residues in contact with LYS 447 (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 THR* 6.4 0.9 - - - -
410A VAL* 6.4 2.2 - - + -
414A ILE* 5.7 1.4 - - - +
441A PRO 4.1 5.3 + - - +
442A GLU* 4.8 8.5 - - - +
443A SER 3.0 19.6 + - - +
444A PRO* 3.0 10.9 + - + +
446A PRO* 1.3 76.4 - - - +
448A PHE* 1.3 62.3 + - - +
450A ARG* 3.4 25.5 - - - +
451A GLU* 3.0 61.2 + - + +
633A THR* 3.4 35.6 + - - -
634A ARG* 4.2 2.0 - - - +
635A LEU* 4.6 5.0 - - - +
742A ASN* 4.7 16.2 - - - +
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Residues in contact with PHE 448 (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 TYR* 4.0 17.5 - + - -
402A LEU* 3.8 19.1 - - + -
410A VAL* 5.0 5.6 - - + -
413A PHE* 3.7 46.2 - + - -
414A ILE* 3.8 24.0 - - + -
417A PHE* 4.2 10.8 - + + -
433A TRP* 4.0 26.9 - + - -
444A PRO 2.8 11.2 + - - +
445A LYS 2.9 11.2 + - - +
447A LYS* 1.3 73.0 - - - +
449A VAL* 1.3 84.1 + - + +
450A ARG 2.9 2.2 + - - -
451A GLU* 3.0 6.6 + - - +
452A VAL* 2.7 48.6 + - + +
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Residues in contact with VAL 449 (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 TYR* 4.4 8.3 - - + -
430A TRP* 3.8 28.0 - - + -
433A TRP* 4.9 5.6 - - + -
436A CYS* 3.7 22.4 - - - -
445A LYS 3.4 15.9 - - - +
446A PRO 3.7 5.4 - - - +
448A PHE* 1.3 87.0 - - + +
450A ARG* 1.3 65.4 + - - +
452A VAL* 3.4 4.0 - - - +
453A LEU* 2.9 45.3 + - + +
473A PHE* 4.2 14.8 - - + -
476A LEU* 4.1 6.7 - - + -
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Residues in contact with ARG 450 (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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441A PRO* 2.6 52.7 + - - +
442A GLU* 4.7 1.4 - - - +
446A PRO 3.0 9.2 + - - +
447A LYS* 3.4 29.5 - - - +
448A PHE 2.9 1.2 + - - -
449A VAL* 1.3 82.5 - - - +
451A GLU* 1.3 66.6 + - + +
452A VAL 2.8 0.5 + - - -
453A LEU* 3.6 1.6 - - - +
454A GLU* 2.9 24.4 + - + +
475A ALA 5.6 0.2 - - - -
476A LEU* 3.5 54.4 - - + +
477A CYS 5.6 0.7 - - - +
478A PRO* 5.6 0.2 - - - +
634A ARG* 5.8 8.7 - - - +
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Residues in contact with GLU 451 (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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414A ILE* 3.6 30.0 - - + +
447A LYS* 3.0 40.9 + - + +
448A PHE 3.0 3.7 + - - +
450A ARG* 1.3 78.9 - - + +
452A VAL* 1.3 62.1 + - - +
454A GLU* 3.3 29.2 - - - +
455A LYS* 3.2 20.1 + - - +
634A ARG* 3.1 17.4 - - - +
635A LEU* 3.0 44.4 + - + +
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Residues in contact with VAL 452 (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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414A ILE* 3.9 20.0 - - + +
417A PHE* 4.3 19.3 - - + -
418A SER* 4.3 3.9 - - - -
421A LEU* 4.4 5.4 - - + -
430A TRP* 4.4 13.5 - - + -
448A PHE* 2.7 53.5 + - + +
449A VAL* 3.4 10.5 - - - +
450A ARG 2.8 1.0 + - - -
451A GLU* 1.3 74.2 - - - +
453A LEU* 1.3 70.5 + - - +
455A LYS* 2.9 15.2 + - - +
456A CYS* 3.0 28.3 + - - -
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Residues in contact with LEU 453 (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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430A TRP* 4.0 18.4 - - + -
449A VAL* 2.9 39.1 + - + +
450A ARG 3.7 2.0 - - - +
452A VAL* 1.3 78.9 - - + +
454A GLU* 1.3 64.1 + - - +
456A CYS* 2.9 22.2 + - - +
457A MET* 3.0 13.7 + - - +
465A ILE* 3.8 21.7 - - + +
468A ILE* 4.4 3.6 - - + -
469A VAL* 3.6 31.9 - - + -
473A PHE* 5.4 5.4 - - + +
476A LEU* 4.1 19.3 - - + +
477A CYS* 5.0 4.0 - - - -
478A PRO* 3.9 12.5 - - + +
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Residues in contact with GLU 454 (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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450A ARG* 2.9 17.1 + - + +
451A GLU* 3.3 28.8 + - - +
453A LEU* 1.3 77.6 - - - +
455A LYS* 1.3 61.3 + - - +
457A MET* 3.5 23.0 - - + +
458A ARG* 3.7 31.4 + - - +
478A PRO* 3.8 20.0 - - + +
598A PRO* 4.3 10.1 - - + +
634A ARG* 3.0 39.6 + - - -
635A LEU* 5.4 0.3 - - - +
636A PHE* 4.4 8.5 + - - +
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Residues in contact with LYS 455 (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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414A ILE* 5.1 4.9 - - + +
415A ASN* 2.8 32.8 - - - +
418A SER* 4.2 19.1 - - - +
451A GLU* 3.2 11.1 + - - +
452A VAL* 2.9 10.5 + - - +
454A GLU* 1.3 77.7 - - - +
456A CYS* 1.3 66.5 + - - +
457A MET 3.1 1.6 - - - -
458A ARG* 3.1 34.0 + - - +
459A LEU* 3.2 17.2 + - + +
635A LEU* 4.1 22.4 - - + +
639A GLU* 3.2 27.3 + - - +
58B GLU* 3.3 27.7 - - - +
62B LYS* 4.8 6.7 - - - +
1555B GOL 5.3 0.2 - - - -
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Residues in contact with CYS 456 (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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418A SER* 3.7 22.0 - - - -
421A LEU* 4.3 6.7 - - - -
426A PHE* 3.3 28.5 - - + -
430A TRP* 6.3 0.2 - - - -
452A VAL* 3.0 27.6 + - - -
453A LEU* 2.9 14.7 + - + +
455A LYS* 1.3 76.2 - - - +
457A MET* 1.3 63.1 + - - +
459A LEU* 2.9 23.3 + - - +
460A SER* 2.9 16.1 + - - -
465A ILE* 3.9 9.6 - - + -
468A ILE* 6.0 0.7 - - + -
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Residues in contact with MET 457 (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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453A LEU 3.0 10.1 + - - +
454A GLU* 3.5 20.0 - - + +
456A CYS* 1.3 77.1 - - - +
458A ARG* 1.3 61.8 + - + +
460A SER* 2.6 41.1 + - - +
461A TYR* 3.1 1.4 + - - +
462A HIS* 3.4 42.4 - - + +
465A ILE* 3.9 18.1 - - + +
478A PRO* 3.4 29.2 - - + -
479A ALA 3.9 8.1 - - - +
481A PRO* 4.3 17.5 - - + -
596A ASN 5.6 1.6 - - - +
597A HIS* 5.5 6.5 - - + +
598A PRO* 5.6 9.4 - - + -
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Residues in contact with ARG 458 (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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454A GLU* 3.7 37.2 + - - +
455A LYS* 3.1 25.6 + - - +
457A MET* 1.3 87.4 - - + +
459A LEU* 1.3 60.4 + - - +
460A SER 3.1 1.8 + - - -
597A HIS* 5.6 2.9 - - + -
598A PRO* 4.1 16.7 - - - +
599A GLN* 3.5 42.5 - - + +
602A ALA* 5.4 1.0 - - - +
636A PHE* 4.3 9.5 - - - +
639A GLU* 3.4 24.9 + - - -
54B GLU 4.7 0.2 - - - -
55B GLN* 3.6 24.1 - - - +
58B GLU* 2.9 31.3 + - - +
1555B GOL 2.7 24.9 + - - -
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Residues in contact with LEU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A SER* 3.9 24.0 - - - +
419A HIS* 4.1 4.7 - - + +
422A SER* 3.5 34.1 - - - +
426A PHE* 4.4 4.1 - - + -
455A LYS* 3.4 15.3 - - + +
456A CYS* 2.9 17.2 + - - +
458A ARG* 1.3 77.3 - - - +
460A SER* 1.3 60.2 + - - +
55B GLN* 4.0 13.4 + - - +
58B GLU* 3.4 30.1 - - + +
59B LEU* 4.6 15.9 - - + +
62B LYS* 4.3 12.3 - - - -
106B LEU* 4.7 12.2 - - + +
107B ASP* 4.8 8.0 + - - -
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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
------------------------------------------------------------
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