Contacts of the helix formed by residues 427 - 436 (chain A) in PDB entry 1J38
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 ARG 427 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A ARG* 4.2 25.6 + - + +
424A ASP* 3.0 23.3 - - - +
425A GLU 3.0 0.2 - - - -
426A ALA* 1.3 79.6 - - - +
428A ILE* 1.3 64.6 + - - +
429A ASN 3.1 2.0 - - - -
430A GLN* 3.2 17.3 + - + +
431A LEU* 3.3 20.5 + - + +
536A PRO* 3.6 18.1 - - - +
538A ASP* 2.8 41.7 + - - +
588A PRO* 3.3 37.1 - - - +
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Residues in contact with ILE 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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276A PRO* 3.7 15.6 - - + +
277A PHE* 3.8 3.8 - - + -
424A ASP 3.8 5.6 - - - +
425A GLU* 3.5 33.4 + - - +
426A ALA 3.3 0.2 - - - -
427A ARG* 1.3 83.8 - - + +
429A ASN* 1.3 56.0 + - - +
430A GLN 3.2 1.1 - - - -
431A LEU* 4.4 10.5 - - + +
432A PHE* 3.1 25.8 + - - +
588A PRO* 4.3 11.7 - - + +
589A LEU* 4.3 6.5 - - + +
592A TRP* 3.5 59.9 - - + +
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Residues in contact with ASN 429 (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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275A SER* 3.9 1.4 - - - -
276A PRO* 3.1 25.0 - - - +
277A PHE* 2.6 53.8 - - - +
280A LYS* 3.9 2.8 - - - +
281A PRO 3.4 25.1 - - - +
282A LEU* 3.9 24.1 - - + +
283A VAL 5.0 0.2 + - - -
420A TYR* 5.8 0.2 - - - -
425A GLU 3.6 7.7 + - - +
426A ALA 3.6 8.2 + - - +
427A ARG 3.1 0.8 - - - -
428A ILE* 1.3 76.5 - - - +
430A GLN* 1.3 62.2 + - - +
432A PHE* 4.8 0.7 - - - -
433A LEU* 3.8 18.4 - - - +
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Residues in contact with GLN 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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283A VAL* 3.3 31.1 - - - +
406A SER* 3.1 33.2 + - - -
407A THR* 4.8 0.4 - - - +
408A PRO* 4.1 19.9 - - + +
420A TYR* 4.6 3.5 + - - +
426A ALA 4.1 8.5 - - - +
427A ARG* 3.2 12.3 + - + +
429A ASN* 1.3 84.0 - - - +
431A LEU* 1.3 67.8 + - + +
432A PHE 3.3 0.7 - - - -
433A LEU* 3.3 14.6 + - - +
434A THR* 3.0 35.1 + - - +
538A ASP* 5.2 10.8 - - + +
585A TYR* 5.7 2.8 + - - +
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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 ARG* 3.3 26.5 + - - +
428A ILE* 4.9 5.2 - - + +
430A GLN* 1.3 75.8 - - + +
432A PHE* 1.3 53.7 + - - +
434A THR* 3.0 10.7 + - - -
435A ALA* 2.8 32.7 + - - +
538A ASP* 3.6 30.1 - - + +
585A TYR* 3.3 36.3 - - + +
586A PHE* 3.4 6.2 - - + -
588A PRO* 3.3 28.9 - - + -
589A LEU* 3.5 28.7 - - + +
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Residues in contact with PHE 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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231A ILE* 4.2 20.4 - - + -
234A TYR* 3.6 30.1 - + - -
235A VAL* 4.1 7.4 - - + -
271A ALA* 6.3 0.2 - - + -
274A VAL* 3.5 31.6 - - + -
275A SER* 4.2 3.6 - - - -
276A PRO* 3.3 24.5 - - + -
428A ILE 3.1 21.3 + - - +
429A ASN* 4.8 1.6 - - - -
430A GLN 3.3 0.4 - - - -
431A LEU* 1.3 81.5 - - - +
433A LEU* 1.3 61.5 + - - +
435A ALA* 3.0 12.6 - - + +
436A LEU* 3.0 43.4 + - + +
589A LEU* 3.7 21.5 - - + +
593A LEU* 4.6 11.2 - - + -
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Residues in contact with LEU 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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268A SER* 3.6 32.3 - - - +
271A ALA* 4.2 20.9 - - + -
282A LEU* 4.9 5.6 - - + -
283A VAL* 3.6 26.5 - - + +
359A GLN* 4.8 6.3 - - - +
429A ASN 3.8 15.1 + - - +
430A GLN* 3.3 29.7 + - - +
431A LEU 3.1 0.4 - - - -
432A PHE* 1.3 76.4 - - - +
434A THR* 1.3 58.4 + - - +
435A ALA 2.9 3.8 - - - -
436A LEU* 2.9 27.9 + - + +
437A ASP* 3.5 10.7 + - - +
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Residues in contact with THR 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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403A LEU* 4.3 10.1 - - + -
406A SER* 5.0 4.7 + - - -
430A GLN* 3.0 22.3 + - - -
431A LEU 3.0 9.1 + - - -
433A LEU* 1.3 75.6 - - - +
435A ALA* 1.3 56.4 + - - +
437A ASP* 3.8 7.6 - - - -
438A LYS* 2.8 48.6 + - + +
515A PHE* 4.7 0.2 - - + -
585A TYR* 3.8 24.3 + - + +
586A PHE* 3.4 17.3 - - + -
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Residues in contact with ALA 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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231A ILE* 3.6 26.2 - - + +
431A LEU 2.8 11.0 + - - +
432A PHE* 3.0 21.3 - - + +
433A LEU 2.9 0.2 - - - -
434A THR* 1.3 78.2 - - - +
436A LEU* 1.3 54.6 + - - +
437A ASP 2.9 6.5 + - - -
439A ILE* 3.3 8.4 + - + +
440A VAL* 2.9 33.8 + - - +
586A PHE* 3.9 11.2 - - + -
589A LEU* 4.5 4.9 - - + -
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Residues in contact with LEU 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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231A ILE* 4.1 7.0 - - + -
235A VAL* 3.7 29.8 - - + -
266A GLN* 3.6 0.9 - - - -
267A TRP* 2.8 58.6 + - + +
268A SER* 3.0 21.3 + - - +
270A ILE* 5.4 0.2 - - + -
271A ALA* 4.5 12.6 - - + -
274A VAL* 3.8 23.3 - - + -
432A PHE* 3.0 29.8 + - + +
433A LEU* 2.9 11.9 + - - +
435A ALA* 1.3 74.0 - - - +
437A ASP* 1.3 58.7 + - - +
440A VAL* 3.4 9.9 - - - -
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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