Contacts of the helix formed by residues 406 - 423 (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 ASN 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A MET 6.0 0.4 - - - -
215A GLN 4.0 12.4 + - - +
216A VAL 2.9 18.0 + - - +
218A THR* 6.1 3.6 - - + -
362A LEU* 4.4 9.1 - - - +
404A THR 3.7 1.4 + - - -
405A MET* 1.3 72.9 - - - +
407A THR* 1.3 64.4 + - - +
408A THR* 2.8 38.7 + - - -
409A CYS* 2.8 21.9 + - - +
410A VAL* 3.0 10.1 + - - +
745A GLU* 3.4 27.4 + - - +
748A GLN* 2.7 33.1 + - - +
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Residues in contact with THR 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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405A MET 3.5 2.6 + - - -
406A ASN* 1.3 70.3 + - - +
408A THR* 1.3 57.5 + - - +
410A VAL* 2.7 32.9 + - + +
411A ASP* 2.9 19.8 + - - +
447A LYS* 6.4 0.9 - - - -
635A LEU* 6.0 0.2 - - + -
741A LYS* 4.2 3.4 - - - +
742A ASN* 3.9 25.5 + - - +
745A GLU* 2.3 46.6 + - - +
746A ARG* 3.7 36.8 - - - +
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Residues in contact with THR 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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362A LEU* 4.0 15.2 - - + +
363A PRO 5.1 1.1 - - - +
406A ASN* 2.8 20.5 + - - -
407A THR* 1.3 75.1 - - - +
409A CYS* 1.3 61.6 + - - +
411A ASP* 3.6 5.5 + - - +
412A ARG* 3.4 44.9 + - - +
745A GLU 4.8 1.7 + - - -
748A GLN* 4.1 8.3 + - - -
749A GLN* 3.7 48.6 - - + +
752A LEU* 4.7 4.7 - - + +
753A GLN* 5.0 4.5 - - + +
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Residues in contact with CYS 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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216A VAL* 4.3 15.9 - - - -
360A PHE* 3.4 57.3 - - + -
362A LEU* 3.9 22.9 - - - -
405A MET* 3.5 14.6 - - + -
406A ASN* 2.8 11.9 + - - +
408A THR* 1.3 76.8 - - - +
410A VAL* 1.3 67.3 + - - +
412A ARG* 3.0 10.3 + - - +
413A PHE* 2.8 18.2 + - - +
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LEU* 5.0 11.2 - - + +
405A MET* 3.7 27.8 - - + +
406A ASN 3.0 15.1 + - - +
407A THR* 2.7 19.6 + - + +
409A CYS* 1.3 75.8 - - - +
411A ASP* 1.3 67.2 + - - +
413A PHE* 2.6 20.7 + - + +
414A ILE* 2.7 37.2 + - + +
444A PRO* 6.5 0.9 - - + -
447A LYS* 6.4 2.0 - - + -
448A PHE* 5.0 10.8 - - + -
741A LYS* 6.0 1.3 - - - -
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Residues in contact with ASP 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A THR* 2.9 16.6 + - - +
408A THR* 3.7 7.6 - - - +
410A VAL* 1.3 75.6 - - - +
412A ARG* 1.3 61.9 + - - +
414A ILE* 2.9 10.7 + - - +
415A ASN* 2.7 40.5 + - - +
635A LEU* 3.2 31.9 - - + +
746A ARG* 3.3 30.9 + - - -
749A GLN* 3.9 11.0 + - - +
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Residues in contact with ARG 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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359A LEU* 2.9 44.3 + - + +
360A PHE* 3.6 14.9 + - + +
361A GLN 3.3 20.0 + - - -
362A LEU* 4.7 1.8 - - - +
363A PRO 3.4 12.3 + - - -
364A ALA* 4.9 0.2 - - - +
365A PRO* 3.3 24.2 - - - +
369A ASP* 3.2 28.5 - - + +
408A THR* 3.4 38.7 + - - +
409A CYS* 3.0 13.1 + - - +
411A ASP* 1.3 80.2 - - - +
413A PHE* 1.3 55.0 + - - +
415A ASN* 3.4 10.5 + - + +
416A TRP* 2.9 30.8 + - - +
753A GLN* 5.5 5.9 - - - +
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Residues in contact with PHE 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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360A PHE* 4.2 17.9 - + + -
395A THR* 4.3 13.7 - - + -
398A LEU* 3.7 37.5 - - + -
399A TYR* 3.9 7.4 - - + -
402A LEU* 3.8 29.4 - - + -
405A MET* 4.5 6.3 - - + -
409A CYS 2.8 11.2 + - - +
410A VAL* 2.6 21.4 + - - +
412A ARG* 1.3 71.9 - - - +
414A ILE* 1.3 58.9 + - - +
416A TRP* 3.1 42.4 + + - +
417A PHE* 3.1 14.2 + - + +
448A PHE* 3.7 33.2 - + + -
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Residues in contact with ILE 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 VAL* 2.7 41.6 + - + +
411A ASP* 3.4 11.0 - - - +
413A PHE* 1.3 72.2 - - - +
415A ASN* 1.3 63.4 + - - +
416A TRP 3.5 0.2 + - - -
418A SER* 3.3 23.4 + - - -
447A LYS* 5.7 1.8 - - + +
448A PHE* 3.8 31.0 - - + -
451A GLU* 3.6 51.6 - - + +
452A VAL* 3.8 9.1 - - - +
455A LYS* 5.1 6.2 - - + +
635A LEU* 4.2 22.4 - - + -
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Residues in contact with ASN 415 (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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369A ASP* 5.6 5.1 - - + +
411A ASP* 2.7 33.9 + - - +
412A ARG* 3.5 11.9 + - + +
414A ILE* 1.3 73.5 - - - +
416A TRP* 1.3 63.4 + - - +
418A SER* 3.1 13.7 + - - -
419A HIS* 3.6 10.2 - - - +
455A LYS* 2.8 39.4 + - - +
635A LEU* 4.7 3.9 - - - +
62B LYS* 4.2 19.2 + - - +
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Residues in contact with TRP 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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356A PHE* 4.0 19.5 - + - -
359A LEU* 4.4 19.5 - - + -
372A TYR* 5.1 1.3 - - + -
373A THR* 3.5 37.7 + - + +
376A LEU* 3.8 22.0 - - + +
391A LEU* 4.0 26.2 - - + -
395A THR* 4.0 15.7 - - + -
398A LEU* 5.0 1.1 - - + -
412A ARG 2.9 17.1 + - - +
413A PHE* 3.1 26.2 + + - +
415A ASN* 1.3 75.1 - - - +
417A PHE* 1.3 84.6 + + + +
419A HIS* 2.9 8.3 + - - +
420A HIS* 2.7 72.4 + + + +
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Residues in contact with PHE 417 (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 THR* 4.1 14.4 - - + -
413A PHE* 3.1 14.8 + + + +
414A ILE 4.6 1.3 - - - +
416A TRP* 1.3 111.2 - + + +
418A SER* 1.3 52.4 + - - +
420A HIS* 3.0 13.1 + + - +
421A LEU* 2.6 81.2 + - + +
428A TRP* 3.9 28.0 - + - -
430A TRP* 4.3 7.4 - + - -
433A TRP* 3.9 24.0 - + - -
448A PHE* 4.2 17.7 - + + -
452A VAL* 4.3 7.9 - - + -
1560A GOL 4.9 5.4 - - - -
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Residues in contact with SER 418 (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 3.3 13.9 + - - -
415A ASN* 3.1 14.4 + - - -
416A TRP 3.3 0.2 - - - -
417A PHE* 1.3 75.9 - - - +
419A HIS* 1.3 71.7 + - - +
421A LEU* 3.0 17.0 + - - +
422A SER* 2.8 26.0 + - - -
426A PHE* 4.5 1.9 - - - -
452A VAL* 4.3 5.1 - - - +
455A LYS* 4.2 21.1 - - - +
456A CYS* 3.7 19.3 - - - -
459A LEU* 3.9 12.6 - - - +
62B LYS* 5.2 1.9 + - - -
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Residues in contact with HIS 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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370A VAL* 4.2 22.6 - - + +
373A THR* 3.9 22.4 + - + +
374A THR* 5.7 4.9 - - + +
415A ASN 3.6 11.2 + - - +
416A TRP* 2.9 9.3 + - - +
418A SER* 1.3 80.6 + - - +
420A HIS* 1.3 64.3 - - - +
422A SER* 2.3 32.2 + - - -
423A ASN* 3.4 22.5 + - - -
459A LEU* 4.2 6.1 - - + -
59B LEU* 3.4 28.9 - - + +
62B LYS* 3.6 31.8 - - + +
101B ILE* 5.8 2.0 - - + -
104B THR* 5.1 5.2 + - + +
105B ARG 5.8 0.4 - - - -
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Residues in contact with HIS 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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373A THR* 3.9 8.1 + - + +
376A LEU* 5.5 1.8 - - + +
377A ILE* 4.1 15.9 - - + +
380A CYS* 4.9 2.9 - - - -
391A LEU* 3.5 14.1 - - + +
416A TRP* 2.7 57.1 + + + +
417A PHE* 3.2 18.4 - + - +
419A HIS* 1.3 73.5 - - - +
421A LEU* 1.3 58.5 + - - +
423A ASN* 3.4 6.2 + - - +
424A PHE* 3.1 61.2 - + - -
1560A GOL 3.3 36.2 + - - -
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Residues in contact with LEU 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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417A PHE* 2.6 66.2 + - + +
418A SER* 3.3 13.5 - - - +
420A HIS* 1.3 68.9 - - - +
422A SER* 1.3 62.0 + - - +
423A ASN 3.1 2.5 - - - -
424A PHE* 2.9 16.4 + - + +
426A PHE* 2.8 52.8 + - + +
427A ARG 4.2 6.5 - - - +
428A TRP* 4.0 18.2 - - + -
430A TRP* 4.2 14.8 - - + -
452A VAL* 4.4 0.9 - - + -
456A CYS* 4.3 11.9 - - - -
1560A GOL 5.0 4.5 - - - +
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Residues in contact with SER 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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418A SER 2.8 12.8 + - - -
419A HIS* 2.3 36.8 + - - -
421A LEU* 1.3 74.2 - - - +
423A ASN* 1.3 62.4 + - - +
424A PHE 3.3 0.2 - - - -
425A GLN 4.7 0.4 - - - -
426A PHE* 3.9 27.6 - - - -
459A LEU* 3.5 18.2 - - - +
105B ARG* 4.1 17.2 - - - +
107B ASP 5.7 0.7 + - - -
108B ASP* 4.3 15.9 + - - +
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Residues in contact with ASN 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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377A ILE* 3.9 31.5 - - + +
419A HIS* 3.4 31.1 + - - -
420A HIS 3.4 9.0 + - - +
421A LEU 3.1 0.6 - - - -
422A SER* 1.3 79.7 - - - +
424A PHE* 1.3 71.8 + - + +
425A GLN* 3.7 4.7 + - - +
104B THR* 3.4 11.6 - - - -
105B ARG* 2.5 65.6 + - + +
110B ILE* 5.6 0.2 - - - +
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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