Contacts of the helix formed by residues 426 - 442 (chain A) in PDB entry 4NTW
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 GLU 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A TYR* 3.8 6.7 - - - -
288A TRP* 5.4 3.5 - - + +
423A LYS* 3.8 50.1 + - + +
424A ALA 4.2 0.2 - - - -
425A TYR* 1.3 76.7 - - - +
427A VAL* 1.3 67.1 + - - +
428A ALA* 3.3 6.3 - - + +
429A GLY* 3.1 8.0 + - - +
430A LEU* 3.0 18.4 + - - +
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Residues in contact with VAL 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 3.7 21.3 + - + +
426A GLU* 1.3 74.8 - - - +
428A ALA* 1.3 63.8 + - - +
430A LEU* 2.9 17.4 + - + +
431A LEU* 3.0 25.2 + - + +
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Residues in contact with ALA 428 (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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426A GLU* 4.6 4.2 - - + +
427A VAL* 1.3 78.0 - - - +
429A GLY* 1.3 62.1 + - - +
431A LEU* 4.0 6.9 - - - +
432A GLY* 3.2 22.9 + - - -
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Residues in contact with GLY 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A TYR* 3.6 18.5 + - - -
426A GLU* 3.1 11.7 + - - +
428A ALA* 1.3 78.8 - - - +
430A LEU* 1.3 57.4 + - - +
432A GLY* 4.4 1.1 - - - -
433A ASP* 3.1 27.3 + - - +
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Residues in contact with LEU 430 (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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65A ARG* 3.4 34.3 - - + +
66A ILE* 4.2 15.9 - - + -
69A TYR* 3.9 30.1 - - + -
70A PHE* 5.6 1.1 - - + -
425A TYR* 3.6 18.3 - - + +
426A GLU 3.0 10.7 + - - +
427A VAL* 2.9 12.6 + - - +
429A GLY* 1.3 75.8 - - - +
431A LEU* 1.3 73.3 + - + +
433A ASP* 3.3 4.2 + - - +
434A ILE* 3.0 39.6 + - + +
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Residues in contact with LEU 431 (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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427A VAL* 3.0 25.1 + - + +
428A ALA* 4.0 5.8 - - - +
430A LEU* 1.3 82.1 - - + +
432A GLY* 1.3 57.9 + - - +
433A ASP 2.9 4.3 - - - -
434A ILE* 2.9 29.7 + - + +
435A GLY* 2.9 13.7 + - - -
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Residues in contact with GLY 432 (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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428A ALA 3.2 13.1 + - - -
429A GLY* 4.4 0.9 - - - -
431A LEU* 1.3 77.9 - - - +
433A ASP* 1.3 58.6 + - - +
435A GLY* 4.2 1.5 - - - -
436A GLY* 3.3 18.0 + - - -
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Residues in contact with ASP 433 (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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65A ARG* 3.5 27.0 + - + -
425A TYR* 2.5 32.9 + - - +
429A GLY 3.1 18.9 + - - +
430A LEU 3.3 3.1 + - - +
431A LEU 2.9 0.2 - - - -
432A GLY* 1.3 77.8 - - - +
434A ILE* 1.3 65.2 + - - +
436A GLY* 3.2 2.3 + - - -
437A GLN* 3.0 33.0 + - - +
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Residues in contact with ILE 434 (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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62A CYS* 3.6 31.1 - - + -
65A ARG* 4.9 8.3 - - + -
66A ILE* 4.1 31.0 - - + -
430A LEU* 3.0 30.8 + - + +
431A LEU* 2.9 16.4 + - + +
433A ASP* 1.3 76.3 - - - +
435A GLY* 1.3 56.8 + - - +
437A GLN* 3.1 7.0 + - - +
438A MET* 2.9 45.4 + - + +
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Residues in contact with GLY 435 (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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431A LEU 2.9 13.5 + - - -
432A GLY* 4.2 2.5 - - - -
434A ILE* 1.3 78.6 - - - +
436A GLY* 1.3 59.9 + - - +
438A MET* 3.8 15.3 + - - +
439A GLY* 3.5 15.2 + - - -
444A ALA 4.8 2.9 - - - +
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Residues in contact with GLY 436 (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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432A GLY 3.3 13.5 + - - -
433A ASP* 3.2 7.5 + - - -
434A ILE 3.1 0.8 - - - -
435A GLY* 1.3 76.9 - - - +
437A GLN* 1.3 66.3 + - - +
439A GLY* 3.8 2.7 + - - -
440A LEU* 3.5 17.7 + - - +
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Residues in contact with GLN 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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58A LEU* 3.2 15.2 - - + +
61A VAL* 3.2 33.0 - - + +
62A CYS* 5.0 1.6 - - - -
65A ARG* 4.9 11.9 + - + +
433A ASP* 3.0 28.0 + - - +
434A ILE* 3.1 10.1 + - - +
436A GLY* 1.3 80.7 + - - +
438A MET* 1.3 64.0 + - - +
439A GLY 3.2 0.7 - - - -
440A LEU* 3.1 19.8 + - - +
441A PHE* 3.0 44.0 + - - -
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Residues in contact with MET 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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58A LEU* 3.8 29.6 - - + -
62A CYS* 5.4 2.2 - - - -
434A ILE* 2.9 36.6 + - + +
435A GLY* 3.9 13.2 - - - +
436A GLY 3.4 0.4 - - - -
437A GLN* 1.3 76.7 - - - +
439A GLY* 1.3 56.6 + - - +
442A ILE* 3.1 27.6 + - + +
443A GLY 3.2 5.4 + - - -
444A ALA* 3.5 23.6 + - + +
449A VAL* 5.3 11.4 - - + -
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Residues in contact with GLY 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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435A GLY 3.5 10.2 + - - -
436A GLY* 3.8 3.8 + - - -
437A GLN 3.2 0.6 - - - -
438A MET* 1.3 79.3 - - - +
440A LEU* 1.3 60.8 - - - +
442A ILE 4.4 0.2 - - - -
443A GLY* 3.4 19.7 + - - -
444A ALA 3.7 15.6 + - - -
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Residues in contact with LEU 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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436A GLY 3.5 14.9 + - - +
437A GLN* 3.1 26.1 + - - +
439A GLY* 1.3 79.4 - - - +
441A PHE* 1.3 84.8 + - + +
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Residues in contact with PHE 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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54A SER* 3.4 37.4 + - - +
57A LEU* 3.5 31.4 - - + -
58A LEU* 3.6 26.9 - - + -
61A VAL* 3.7 23.8 - - + -
437A GLN* 3.0 48.6 + - - +
438A MET 4.4 0.2 - - - +
440A LEU* 1.3 95.9 - - + +
442A ILE* 1.3 64.3 + - + +
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Residues in contact with ILE 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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51A PHE* 3.9 35.0 - - + -
54A SER* 4.1 13.9 - - - +
55A LEU* 3.6 31.4 - - + -
58A LEU* 4.1 10.8 - - + -
438A MET* 3.1 8.6 + - + +
441A PHE* 1.3 84.6 - - + +
443A GLY* 1.3 60.8 + - - +
444A ALA* 4.0 20.2 - - + +
448A THR* 6.3 1.3 - - + -
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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
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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