Contacts of the helix formed by residues 436 - 451 (chain A) in PDB entry 3N51
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 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A SER* 4.4 11.9 - - - +
350A LYS* 5.5 4.5 - - + +
353A SER* 3.6 33.0 - - - +
432A MET 3.2 14.2 + - - +
433A ASP* 4.0 3.1 + - - -
434A ARG 2.8 1.6 + - - -
435A LYS* 1.3 73.8 - - + +
437A LEU* 1.3 66.2 + - - +
438A LEU 3.4 0.7 - - - -
439A SER* 2.9 26.1 + - - +
440A ARG* 2.8 41.1 + - - +
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Residues in contact with LEU 437 (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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434A ARG* 2.6 27.0 + - + +
435A LYS 3.1 1.8 - - - -
436A THR* 1.3 69.4 - - - +
438A LEU* 1.3 55.1 + - - +
440A ARG* 2.7 49.1 + - - +
441A GLU* 2.8 60.3 + - + +
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Residues in contact with LEU 438 (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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435A LYS 4.3 6.3 + - - +
436A THR 3.4 0.6 - - - -
437A LEU* 1.3 79.2 - - - +
439A SER* 1.3 58.3 + - - +
441A GLU* 4.9 4.9 - - - +
442A ARG* 3.0 47.5 + - + +
445A ARG* 4.1 17.4 + - - +
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Residues in contact with SER 439 (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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342A ALA 5.1 0.9 - - - +
345A LEU 4.4 3.1 - - - -
346A TYR* 4.3 14.0 - - - +
349A SER* 3.4 36.0 - - - -
436A THR* 2.9 24.4 + - - -
438A LEU* 1.3 79.7 - - - +
440A ARG* 1.3 58.1 + - - +
441A GLU 3.4 0.2 - - - -
442A ARG* 3.7 24.3 + - - +
443A LEU* 2.9 28.6 + - - +
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Residues in contact with ARG 440 (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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346A TYR* 3.7 28.5 - - + -
433A ASP* 2.7 28.5 + - - -
434A ARG* 3.0 19.6 + - - +
436A THR* 2.8 35.7 + - - +
437A LEU* 2.7 43.5 + - - +
439A SER* 1.3 73.1 + - - +
441A GLU* 1.3 59.6 + - + +
443A LEU* 3.6 4.4 + - - +
444A GLU* 3.3 23.7 + - - +
494A PHE* 4.3 6.4 - - - -
498A GLN* 4.4 9.6 - - - +
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Residues in contact with GLU 441 (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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437A LEU* 2.8 60.4 + - + +
438A LEU* 4.5 3.6 + - - +
440A ARG* 1.3 70.9 - - + +
442A ARG* 1.3 62.0 + - - +
443A LEU 3.1 1.3 - - - -
444A GLU* 3.4 9.0 + - - +
445A ARG* 2.9 53.3 + - - +
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Residues in contact with ARG 442 (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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341A GLN* 6.4 0.4 - - - -
342A ALA* 4.5 16.0 + - + +
345A LEU* 3.3 48.1 + - - +
346A TYR 5.0 0.2 - - - +
349A SER* 4.9 1.2 + - - -
438A LEU* 3.0 43.5 + - + +
439A SER* 3.7 25.9 + - - +
441A GLU* 1.3 79.1 - - - +
443A LEU* 1.3 56.3 + - - +
445A ARG* 3.5 20.4 + - + +
446A ALA* 3.0 28.0 + - + +
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Residues in contact with LEU 443 (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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339A LEU* 4.3 3.6 - - + -
342A ALA* 3.8 12.3 - - + +
343A ALA* 3.8 34.3 - - - +
346A TYR* 3.9 24.2 - - + -
439A SER 2.9 20.3 + - - +
440A ARG* 3.7 4.9 - - - +
441A GLU 3.1 0.4 - - - -
442A ARG* 1.3 76.3 - - - +
444A GLU* 1.3 56.2 + - - +
446A ALA* 3.2 4.2 + - - +
447A PHE* 3.0 26.3 + - - +
494A PHE* 3.9 24.2 - - + -
497A PHE* 4.1 12.8 - - + -
498A GLN* 4.5 8.7 - - + +
501A LEU* 3.8 22.9 - - + -
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Residues in contact with GLU 444 (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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440A ARG 3.3 11.5 + - - +
441A GLU* 3.8 8.7 - - - +
443A LEU* 1.3 76.5 - - - +
445A ARG* 1.3 60.3 + - + +
447A PHE* 3.2 2.1 + - - +
448A ARG* 2.7 75.4 + - + +
494A PHE* 3.6 33.9 - - + -
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Residues in contact with ARG 445 (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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438A LEU* 4.1 18.2 + - - +
441A GLU* 2.9 49.4 + - - +
442A ARG* 3.5 30.2 - - + +
444A GLU* 1.3 73.5 - - - +
446A ALA* 1.3 57.2 + - - +
448A ARG* 3.5 7.1 + - - +
449A MET* 3.0 35.8 + - + +
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Residues in contact with ALA 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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335A GLY 4.8 1.6 - - - +
338A LYS* 4.1 10.3 - - + +
339A LEU* 3.8 26.7 - - + +
342A ALA* 3.8 16.4 - - + -
442A ARG* 3.0 19.1 + - + +
443A LEU 3.2 4.4 + - - +
445A ARG* 1.3 73.4 - - - +
447A PHE* 1.3 60.1 + - - +
449A MET* 3.4 7.2 + - - +
450A PHE* 2.9 30.8 + - - +
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Residues in contact with PHE 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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339A LEU* 3.7 12.0 - - + +
443A LEU 3.0 13.0 + - - +
444A GLU 3.5 6.7 - - - +
446A ALA* 1.3 75.4 - - - +
448A ARG* 1.3 90.8 + - - +
450A PHE* 3.3 4.2 + - - +
451A ASP* 3.0 31.4 + - + +
456A GLY 3.9 20.4 - - - -
457A LYS 4.6 0.2 - - - -
458A ILE* 3.1 43.7 - - + -
492A VAL 4.1 2.9 - - - -
493A ASP 3.8 5.4 - - - -
494A PHE* 3.5 47.1 - + + -
497A PHE* 4.0 20.9 - + + -
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Residues in contact with ARG 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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444A GLU* 2.7 60.1 + - + +
445A ARG* 3.8 7.0 - - - +
447A PHE* 1.3 92.9 - - - +
449A MET* 1.3 62.9 + - - +
451A ASP* 3.2 27.7 + - - +
452A SER* 5.0 0.2 - - - -
454A ASN* 5.0 1.7 - - - +
456A GLY* 4.7 13.1 + - - -
494A PHE* 3.7 23.6 - - - +
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Residues in contact with MET 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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138A ASP* 6.2 0.2 - - - +
141A ILE* 4.7 23.6 - - + -
335A GLY* 5.4 10.2 - - - -
338A LYS* 6.4 3.1 - - + -
445A ARG* 3.0 22.1 + - + +
446A ALA* 3.6 7.6 - - - +
447A PHE 3.3 0.2 - - - -
448A ARG* 1.3 74.9 - - - +
450A PHE* 1.3 65.3 + - - +
451A ASP 3.3 0.3 + - - -
452A SER* 3.9 12.1 + - - -
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Residues in contact with PHE 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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332A GLN* 4.8 5.8 - - + -
335A GLY* 3.8 12.4 - - - +
336A THR* 3.3 45.5 - - + -
339A LEU* 3.7 20.6 - - + -
446A ALA 2.9 21.5 + - - +
447A PHE 3.6 4.0 - - - +
449A MET* 1.3 72.2 - - - +
451A ASP* 1.3 60.1 + - - +
452A SER* 2.9 13.4 + - - -
457A LYS 5.9 0.4 - - - -
458A ILE* 4.1 19.1 - - + -
462A GLU* 3.6 52.7 - - + +
465A THR* 6.3 0.4 - - - -
466A ILE* 3.9 12.3 - - + -
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Residues in contact with ASP 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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447A PHE* 3.0 24.3 + - + +
448A ARG* 3.3 19.7 + - - +
449A MET 3.2 1.0 - - - -
450A PHE* 1.3 76.1 - - + +
452A SER* 1.3 57.7 + - - +
453A ASP* 3.0 22.6 - - - +
454A ASN* 3.0 27.6 + - - +
455A SER* 3.0 17.4 + - - -
456A GLY* 2.6 34.2 + - - -
457A LYS 3.9 9.1 - - - +
458A ILE* 5.8 0.9 - - + -
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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