Contacts of the helix formed by residues 538 - 552 (chain A) in PDB entry 1IGN
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 538 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526A PHE* 3.6 29.0 - - + +
527A LYS* 3.5 33.1 + - + +
530A ALA* 3.5 16.7 - - + +
537A THR* 1.3 74.3 - - - +
539A ASN* 1.3 63.8 + - - +
541A TRP* 3.5 3.1 + - - +
542A ARG* 3.0 31.8 + - + +
20D C 3.3 34.8 + - - +
21D C 4.5 2.1 + - - -
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Residues in contact with ASN 539 (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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537A THR* 3.2 1.0 + - - -
538A GLU* 1.3 82.4 - - - +
540A ALA* 1.3 66.1 + - - +
542A ARG* 3.4 5.5 + - - +
543A ASP* 3.0 25.3 + - - +
14C C 4.0 3.8 - - + -
15C A 3.3 72.0 + - + +
16C C 4.3 16.3 + - - -
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Residues in contact with ALA 540 (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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449A PHE* 3.6 10.8 - - + -
536A HIS* 3.9 9.9 - - + -
537A THR* 3.2 19.3 + - - +
539A ASN* 1.3 80.1 - - - +
541A TRP* 1.3 58.5 + - - +
543A ASP* 3.4 1.8 + - - +
544A ARG* 2.9 29.6 + - - +
13C A 4.3 3.1 - - + +
14C C 3.0 46.4 - - + +
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Residues in contact with TRP 541 (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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449A PHE* 3.8 18.2 - + - -
453A GLU* 3.7 46.0 - - + -
454A ASP* 5.5 0.4 - - - -
456A THR* 5.7 1.1 - - - -
457A LEU* 4.0 21.6 - - + +
526A PHE* 3.9 16.9 - - + +
529A PHE* 3.6 36.7 - + + -
530A ALA* 3.8 17.7 - - + +
533A HIS* 3.0 36.2 + + + -
535A ALA* 5.2 2.0 - - + -
536A HIS* 3.2 32.2 + + + +
537A THR 3.1 25.8 + - - +
538A GLU* 3.9 4.3 - - - +
540A ALA* 1.3 76.6 - - - +
542A ARG* 1.3 63.1 + - - +
544A ARG* 3.3 3.9 + - - +
545A PHE* 3.0 23.2 + - - +
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Residues in contact with ARG 542 (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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526A PHE* 3.6 39.1 - - + -
538A GLU* 3.0 22.3 + - + +
539A ASN* 3.8 5.8 - - - +
540A ALA 3.3 0.2 - - - -
541A TRP* 1.3 76.9 - - - +
543A ASP* 1.3 57.8 + - - +
545A PHE* 3.2 4.6 + - - +
546A ARG* 2.9 53.8 + - + +
16C C 4.7 6.1 - - - +
17C C 4.8 0.4 - - - +
21D C 5.9 1.6 - - - -
22D T 3.5 49.7 + - - +
23D G 2.8 45.5 + - - -
24D G 4.3 0.6 + - - -
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Residues in contact with ASP 543 (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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539A ASN 3.0 17.3 + - - +
540A ALA 4.0 2.0 - - - +
542A ARG* 1.3 74.3 - - - +
544A ARG* 1.3 60.5 + - - +
546A ARG* 4.2 8.3 + - - +
547A LYS* 2.8 75.2 + - - +
548A PHE* 5.3 0.7 - - - -
13C A 4.1 8.6 + - + +
14C C 3.0 40.0 + - + -
15C A 3.7 11.8 + - - +
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Residues in contact with ARG 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A PHE* 3.4 44.6 - - + +
454A ASP* 2.8 43.3 + - - +
457A LEU* 4.2 12.8 - - + -
540A ALA 2.9 18.8 + - - +
541A TRP* 3.5 6.1 - - - +
543A ASP* 1.3 76.9 - - - +
545A PHE* 1.3 58.0 + - - +
548A PHE* 3.2 39.4 + - + +
549A LEU* 3.0 22.5 + - - +
573A PRO* 4.1 3.4 - - - +
574A MET* 2.8 27.8 + - + +
575A LYS* 5.8 0.6 - - - +
13C A 2.9 33.1 + - - -
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Residues in contact with PHE 545 (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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457A LEU* 4.1 7.8 - - + +
461A VAL* 3.9 28.3 - - + -
518A ARG 3.4 24.7 - - - -
521A ILE* 3.6 24.7 - - + -
526A PHE* 3.4 24.9 - + + -
541A TRP 3.0 13.3 + - - +
542A ARG* 3.5 9.4 - - - +
544A ARG* 1.3 78.6 - - - +
546A ARG* 1.3 68.6 + - + +
549A LEU* 3.3 24.5 + - + +
550A LEU* 2.8 62.0 + - + +
554A ILE* 4.5 3.6 - - + -
22D T 5.8 0.7 - - - -
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Residues in contact with ARG 546 (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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518A ARG* 4.5 9.0 + - - +
542A ARG* 2.9 48.3 + - + +
543A ASP* 3.2 12.5 + - - +
545A PHE* 1.3 92.8 - - + +
547A LYS* 1.3 87.0 + - - +
550A LEU* 3.5 25.2 - - + +
551A ALA* 4.2 2.8 + - - +
15C A 4.5 1.2 - - - +
16C C 5.0 0.2 - - - +
23D G 3.3 42.1 + - - +
24D G 2.7 49.9 + - - -
25D T 4.0 6.1 + - - +
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Residues in contact with LYS 547 (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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543A ASP* 2.8 56.6 + - - +
546A ARG* 1.3 103.5 - - - +
548A PHE* 1.3 73.3 + - + +
551A ALA* 3.1 18.4 - - - +
577A LEU* 3.8 16.7 - - - +
578A THR* 5.7 5.6 - - - +
14C C 5.0 0.6 - - - +
25D T 2.7 38.2 + - + +
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Residues in contact with PHE 548 (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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543A ASP 5.9 0.2 - - - -
544A ARG* 3.2 41.5 + - - +
547A LYS* 1.3 96.6 - - + +
549A LEU* 1.3 63.2 + - - +
550A LEU 3.4 0.4 - - - -
551A ALA* 3.2 3.1 + - - +
552A TYR* 2.8 33.4 + - - +
574A MET* 3.5 21.7 - - + +
575A LYS* 4.0 6.7 - - - -
577A LEU* 3.6 30.0 - - + +
578A THR* 4.1 6.3 - - - -
12C C 3.5 56.3 - - + -
13C A 3.4 16.6 - - - -
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Residues in contact with LEU 549 (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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454A ASP 4.9 0.7 - - - +
457A LEU* 4.0 14.4 - - + -
458A ALA* 3.6 45.1 - - + +
461A VAL* 4.4 3.1 - - + -
544A ARG 3.0 4.6 + - - +
545A PHE* 3.3 34.1 + - + +
548A PHE* 1.3 77.3 - - - +
550A LEU* 1.3 56.6 + - - +
553A GLY* 2.7 38.5 + - - -
554A ILE* 3.7 26.9 + - + -
557A TYR* 4.3 9.2 - - + -
574A MET* 3.6 26.1 - - + -
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Residues in contact with LEU 550 (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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517A ARG 4.4 6.3 - - - +
518A ARG* 3.2 61.9 - - + +
545A PHE* 2.8 58.2 + - + +
546A ARG* 3.5 18.2 - - + +
548A PHE 3.4 0.2 - - - -
549A LEU* 1.3 72.8 - - - +
551A ALA* 1.3 61.9 + - - +
553A GLY* 3.9 7.3 + - - -
554A ILE* 4.4 10.8 - - + -
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Residues in contact with ALA 551 (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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546A ARG 4.2 2.7 + - - +
547A LYS 3.1 26.5 - - - +
548A PHE* 3.2 4.9 + - - +
549A LEU 3.1 0.2 - - - -
550A LEU* 1.3 78.7 - - - +
552A TYR* 1.3 62.4 + - - +
577A LEU* 4.3 17.9 - - + +
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Residues in contact with TYR 552 (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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548A PHE 2.8 18.5 + - - +
549A LEU 4.2 0.2 - - - +
551A ALA* 1.3 74.4 - - - +
553A GLY* 1.3 56.5 + - - +
556A ASP* 3.5 22.3 - - + +
557A TYR* 3.2 52.3 - + + -
560A TYR* 3.3 33.1 - + - +
574A MET* 3.8 22.9 - - + -
577A LEU* 4.6 18.2 - - + -
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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
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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