Contacts of the strand formed by residues 413 - 426 (chain A) in PDB entry 1NQF
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 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ASN* 5.5 0.2 + - - -
74A SER* 5.1 1.2 + - - -
75A HIS* 3.4 22.5 + - + +
123A ILE* 4.7 2.2 - - - +
393A TYR* 3.1 6.4 - - - +
394A LYS* 2.8 50.4 + - + +
395A ALA 6.4 0.4 - - - -
400A GLN* 4.6 3.7 - - - +
412A PRO* 1.3 71.8 - - - +
414A LYS* 1.3 59.8 + - - +
440A VAL* 5.0 2.5 - - + -
441A SER 3.4 7.9 - - - +
442A ASP 3.0 17.9 - - - +
443A LEU* 3.5 19.9 - - + +
444A ILE* 2.6 46.7 + - + +
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Residues in contact with LYS 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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368A HIS* 3.7 29.8 - - + +
392A SER 3.4 6.3 - - - +
411A ASP* 6.5 0.4 - - + -
412A PRO* 3.4 19.5 - - + +
413A GLU* 1.3 74.8 - - - +
415A SER* 1.3 61.7 + - - +
416A LYS* 5.1 14.5 - - + +
439A ASP 3.8 1.0 - - - +
440A VAL* 3.4 3.2 - - - -
441A SER* 2.7 51.3 + - - +
442A ASP* 2.9 27.1 - - - +
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Residues in contact with SER 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.9 18.3 - - - +
391A THR* 3.3 7.1 + - - -
392A SER* 2.7 57.8 + - - +
414A LYS* 1.3 76.3 - - - +
416A LYS* 1.3 69.4 + - - +
417A GLN* 3.6 6.4 + - - +
438A ASN* 3.0 26.2 + - - -
439A ASP 3.4 3.1 - - - -
440A VAL* 3.9 8.3 - - - -
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Residues in contact with LYS 416 (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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389A TYR* 3.7 25.6 + - + +
390A GLY 3.4 4.7 - - - +
391A THR* 4.0 8.5 - - - +
414A LYS* 5.1 13.9 - - + +
415A SER* 1.3 79.2 - - - +
417A GLN* 1.3 61.4 + - - +
418A TRP* 3.8 27.7 - - + -
437A ARG 3.8 0.7 - - - +
438A ASN* 3.0 4.2 - - - +
439A ASP* 2.8 39.1 + - + +
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Residues in contact with GLN 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 4.5 8.5 + - - -
112A GLY* 3.7 8.8 - - - -
113A PRO* 3.0 46.6 - - + +
123A ILE* 4.0 3.8 - - - +
124A GLY* 3.2 27.2 - - - +
388A SER 4.0 0.3 - - - +
389A TYR* 3.3 7.7 - - - -
390A GLY 2.9 30.7 + - - -
392A SER* 4.2 0.2 + - - -
415A SER* 3.6 10.5 + - - +
416A LYS* 1.3 72.6 - - - +
418A TRP* 1.3 64.8 + - - +
419A GLU* 5.3 1.5 - - + +
436A TYR* 5.1 8.1 - - + +
437A ARG 3.4 4.7 - - - +
438A ASN* 3.4 35.8 + - + +
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Residues in contact with TRP 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A SER 3.5 7.0 - - - +
389A TYR* 3.7 31.5 - + + -
416A LYS* 3.8 37.0 - - + -
417A GLN* 1.3 80.0 - - - +
419A GLU* 1.3 63.0 + - - +
436A TYR* 3.3 3.1 - - - +
437A ARG* 2.9 71.5 + - + +
439A ASP* 3.9 27.1 - - - -
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Residues in contact with GLU 419 (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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25A PRO* 3.7 15.1 - - - +
69A ARG* 3.1 37.0 + - - -
111A ARG 4.7 2.1 - - - +
112A GLY* 4.9 3.5 - - - -
386A ILE 4.5 0.2 - - - -
387A ALA* 3.5 4.3 - - - +
388A SER* 3.0 44.1 + - - +
417A GLN* 5.3 2.0 - - + +
418A TRP* 1.3 78.1 - - - +
420A GLY* 1.3 63.6 + - - +
421A ALA* 4.7 2.2 - - + +
432A ARG* 5.2 0.9 + - - -
434A SER* 3.1 26.6 + - - -
435A GLY 3.2 17.9 - - - +
436A TYR* 3.8 7.9 - - + +
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Residues in contact with GLY 420 (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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385A PHE* 4.7 10.8 - - - -
386A ILE 3.3 6.3 - - - -
387A ALA* 4.7 1.6 - - - -
419A GLU* 1.3 74.5 - - - +
421A ALA* 1.3 64.5 + - - +
434A SER* 3.2 1.9 - - - -
435A GLY* 3.0 31.9 + - - -
804A C8E 4.6 8.4 - - - +
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Residues in contact with ALA 421 (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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384A ARG 3.9 0.2 - - - +
385A PHE* 3.0 11.7 - - - -
386A ILE* 2.8 47.7 + - + +
419A GLU* 4.7 2.7 - - + +
420A GLY* 1.3 76.7 - - - +
422A PHE* 1.3 65.0 + - - +
423A GLU* 4.2 0.7 - - + -
432A ARG* 4.2 20.6 - - - +
433A ILE 3.3 7.0 - - - +
434A SER* 3.2 23.3 - - - +
804A C8E 5.5 1.6 - - - -
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Residues in contact with PHE 422 (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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379A PHE* 3.9 20.2 - + - -
384A ARG 3.4 3.4 - - - -
385A PHE* 3.1 44.0 - + + -
421A ALA* 1.3 71.2 - - - +
423A GLU* 1.3 61.5 + - - +
431A TRP* 3.5 12.8 - - + -
432A ARG* 3.4 2.9 - - - +
433A ILE* 3.0 37.6 + - + -
801A C8E 3.2 40.6 - - + -
804A C8E 4.8 16.6 - - + -
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Residues in contact with GLU 423 (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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382A GLY 4.5 0.4 - - - -
383A TYR* 3.5 4.7 - - - +
384A ARG* 3.0 66.7 + - + +
386A ILE* 4.0 6.9 - - + +
421A ALA 5.5 0.2 - - - -
422A PHE* 1.3 76.3 - - - +
424A GLY* 1.3 61.5 + - - +
431A TRP* 3.5 18.6 - - - +
432A ARG* 2.6 45.1 + - + +
801A C8E 5.7 0.2 - - - +
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Residues in contact with GLY 424 (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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382A GLY 3.2 11.0 - - - -
383A TYR* 4.1 4.7 - - - -
423A GLU* 1.3 79.1 - - - +
425A LEU* 1.3 59.6 + - - -
429A VAL 3.5 0.2 - - - +
430A ASN* 3.5 5.6 - - - +
431A TRP* 3.0 56.6 + - - +
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Residues in contact with LEU 425 (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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382A GLY* 3.1 20.7 + - - +
383A TYR* 3.4 15.3 + - - -
424A GLY* 1.3 71.5 - - - -
426A THR* 1.3 63.8 + - - +
428A GLY* 4.2 10.8 - - - +
429A VAL 3.3 21.5 - - - +
430A ASN* 3.5 27.8 - - - +
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Residues in contact with THR 426 (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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383A TYR* 3.1 27.8 - - + +
425A LEU* 1.3 71.9 - - - +
427A ALA* 1.3 76.5 + - - +
428A GLY 2.8 1.6 - - - -
429A VAL* 2.6 39.2 + - + +
431A TRP* 2.7 41.1 - - + +
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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