Contacts of the helix formed by residues 461 - 481 (chain A) in PDB entry 5IWM
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 ASP 461 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A THR* 3.5 8.4 + - + +
458A ILE 2.9 19.1 + - - +
459A LEU 3.4 1.1 - - - -
460A ALA* 1.3 79.1 - - - +
462A GLU* 1.3 63.3 + - - +
463A GLU* 3.0 22.8 + - - +
464A VAL* 3.2 36.1 + - + +
465A LEU* 3.4 2.9 + - - +
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Residues in contact with GLU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LYS* 5.8 4.0 - - - -
364A ARG* 2.6 42.0 + - - -
459A LEU 4.9 4.7 - - - +
460A ALA 4.3 0.8 - - - -
461A ASP* 1.3 73.1 + - - +
463A GLU* 1.3 57.0 + - - +
464A VAL 3.4 0.2 - - - -
465A LEU* 3.6 10.8 + - - +
466A LEU* 3.2 28.1 + - - +
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Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ASP* 3.0 14.3 + - - +
462A GLU* 1.3 76.9 - - - +
464A VAL* 1.3 61.1 + - + +
466A LEU* 4.5 11.4 - - - +
467A GLN* 3.0 29.7 + - + +
470A ARG* 3.0 35.6 + - - -
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Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A THR* 5.0 10.5 - - + +
458A ILE* 3.9 30.2 - - + +
461A ASP* 3.2 33.9 + - + +
463A GLU* 1.3 76.1 - - + +
465A LEU* 1.3 57.0 + - - +
467A GLN* 3.9 6.2 - - + +
468A LEU* 3.1 26.9 + - + +
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LYS* 4.3 13.2 - - + +
363A VAL* 3.7 28.3 - - + +
364A ARG* 3.3 62.6 - - + +
367A THR* 4.9 1.1 - - - +
458A ILE* 4.1 26.1 + - + +
459A LEU* 5.6 2.9 - - + -
461A ASP 3.4 9.5 + - - +
462A GLU* 3.8 12.6 - - - +
463A GLU 3.3 0.2 - - - -
464A VAL* 1.3 77.6 - - - +
466A LEU* 1.3 64.5 + - - +
468A LEU* 3.2 7.6 + - + +
469A VAL* 3.2 23.4 + - + +
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Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 3.9 28.5 - - - +
356A LEU* 4.4 8.1 - - + -
360A LYS* 4.2 37.2 - - + +
462A GLU 3.2 14.9 + - - +
463A GLU* 4.1 14.6 - - - +
464A VAL 3.5 0.2 - - - -
465A LEU* 1.3 76.2 - - - +
467A GLN* 1.3 66.1 + - - +
469A VAL* 3.1 12.9 + - + +
470A ARG* 3.1 51.2 + - + +
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Residues in contact with GLN 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A GLU* 3.0 21.8 + - + +
464A VAL* 3.9 7.0 - - + +
466A LEU* 1.3 76.8 - - - +
468A LEU* 1.3 56.9 + - - +
470A ARG* 2.9 45.9 + - - +
471A ASP* 2.9 62.1 + - - +
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Residues in contact with LEU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL* 3.9 12.8 - - + -
366A ARG* 3.7 19.7 - - - +
367A THR* 4.7 3.4 - - - +
458A ILE* 4.0 33.4 - - + -
464A VAL* 3.1 15.2 + - + +
465A LEU 3.3 10.1 - - - +
466A LEU 3.2 0.2 - - - -
467A GLN* 1.3 75.3 - - - +
469A VAL* 1.3 63.2 + - - +
471A ASP* 3.5 13.2 + - + +
472A GLU* 3.1 42.8 + - + +
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Residues in contact with VAL 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ARG* 5.1 1.5 + - - +
356A LEU* 4.5 11.9 - - + -
359A GLN* 3.9 32.5 - - + +
360A LYS* 4.4 9.2 - - + -
363A VAL* 3.8 32.5 - - + -
465A LEU* 3.2 16.3 + - + +
466A LEU* 3.1 15.1 + - + +
468A LEU* 1.3 75.2 - - - +
470A ARG* 1.3 59.1 + - + +
472A GLU* 3.3 4.6 + - - +
473A LEU* 2.8 48.8 + - + +
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Residues in contact with ARG 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 4.0 19.5 - - + +
199A SER* 3.1 51.1 + - - +
200A LYS* 4.1 24.7 - - - +
463A GLU* 3.0 28.7 + - - -
466A LEU* 3.1 29.0 + - + +
467A GLN* 2.9 45.5 + - - +
469A VAL* 1.3 76.1 - - + +
471A ASP* 1.3 51.0 + - - +
473A LEU* 3.2 4.7 + - + +
474A THR* 2.6 42.0 + - - +
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Residues in contact with ASP 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A GLN* 2.9 41.0 + - - +
468A LEU* 3.8 14.9 - - + +
469A VAL 3.4 0.2 - - - -
470A ARG* 1.3 74.6 - - - +
472A GLU* 1.3 59.6 + - + +
474A THR* 3.3 7.5 + - - -
475A GLU* 2.9 30.0 + - - +
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Residues in contact with GLU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG* 2.9 16.7 + - - +
163A ARG* 2.5 53.1 + - - +
363A VAL* 5.0 1.3 - - - -
366A ARG* 2.8 33.5 + - - -
468A LEU* 3.1 29.3 + - + +
469A VAL 3.9 2.0 - - - +
471A ASP* 1.3 76.0 - - + +
473A LEU* 1.3 61.6 + - - +
475A GLU* 3.5 7.6 + - - +
476A ILE* 3.0 30.8 + - - +
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Residues in contact with LEU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ARG* 3.6 24.5 - - - +
165A PRO* 4.8 6.7 - - + -
192A ILE* 3.6 25.2 - - + +
195A VAL* 3.6 30.7 - - + -
196A LEU* 4.4 10.5 - - + -
355A TYR* 3.8 20.4 - - + +
356A LEU* 4.9 2.5 - - + -
359A GLN* 4.7 6.3 - - + +
469A VAL* 2.8 39.4 + - + +
470A ARG* 3.5 5.4 - - + +
472A GLU* 1.3 76.1 - - + +
474A THR* 1.3 60.4 + - - +
476A ILE* 3.1 7.1 + - - +
477A ARG 2.9 23.6 + - - -
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Residues in contact with THR 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 4.4 2.6 - - - +
196A LEU* 4.0 14.7 - - - +
470A ARG* 2.6 30.8 + - - +
471A ASP* 3.6 9.0 + - - -
473A LEU* 1.3 72.0 - - - +
475A GLU* 1.3 57.5 + - - +
477A ARG* 3.3 37.5 - - - +
478A ASP* 3.0 37.2 + - - +
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Residues in contact with GLU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG* 4.3 7.9 + - - -
471A ASP 2.9 17.3 + - - +
472A GLU* 3.6 8.5 - - - +
474A THR* 1.3 76.0 - - - +
476A ILE* 1.3 71.0 + - - +
478A ASP* 3.6 6.6 + - - +
479A ARG* 3.2 59.5 + - - +
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Residues in contact with ILE 476 (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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131A ILE* 5.7 0.4 - - + -
134A GLU* 3.2 39.3 - - + +
137A ARG* 4.3 6.1 - - - +
163A ARG* 3.8 21.5 - - + +
164A PHE* 4.0 25.1 - - + -
188A LEU* 4.4 6.7 - - + -
192A ILE* 4.1 9.4 - - + -
472A GLU 3.0 18.7 + - - +
473A LEU* 3.1 7.1 + - - +
475A GLU* 1.3 82.4 - - - +
477A ARG* 1.3 59.7 + - - +
479A ARG* 3.1 2.9 + - - +
480A PHE* 2.7 51.7 + - + +
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Residues in contact with ARG 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 5.4 0.9 - - - -
189A THR* 4.2 29.6 - - + +
192A ILE* 3.6 25.7 - - + +
193A ASN* 3.0 33.9 + - - +
196A LEU* 3.8 16.2 - - - +
473A LEU 2.9 12.6 + - - +
474A THR* 3.3 29.2 + - - +
476A ILE* 1.3 75.8 - - - +
478A ASP* 1.3 79.9 + - - +
481A GLY* 2.6 36.9 + - - +
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Residues in contact with ASP 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A THR* 3.0 31.3 + - - +
475A GLU* 4.1 5.9 - - - +
477A ARG* 1.3 97.7 + - - +
479A ARG* 1.3 59.5 + - - +
481A GLY 4.7 4.0 + - - +
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Residues in contact with ARG 479 (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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130A LYS* 5.4 1.4 + - - +
134A GLU* 2.7 30.5 + - - -
137A ARG* 4.4 4.6 - - - +
475A GLU* 3.2 47.7 + - - +
476A ILE* 3.1 4.9 + - - +
478A ASP* 1.3 79.2 - - - +
480A PHE* 1.3 93.6 + - + +
481A GLY 5.2 0.7 - - - -
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Residues in contact with PHE 480 (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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101A TYR* 4.4 6.6 - - - -
130A LYS* 3.8 30.1 - - + -
131A ILE* 3.8 37.2 - - + -
134A GLU* 3.7 15.5 - - + -
188A LEU* 3.9 21.0 - - + +
476A ILE* 2.7 35.0 + - + +
479A ARG* 1.3 119.5 - - + +
481A GLY* 1.3 63.5 + - - +
482A ASP* 3.5 10.2 + - - +
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Residues in contact with GLY 481 (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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188A LEU* 4.5 4.4 - - - +
189A THR* 3.2 23.6 - - - -
476A ILE 3.9 0.2 + - - -
477A ARG* 2.6 29.8 + - - +
478A ASP 4.9 4.0 - - - +
479A ARG 3.8 0.7 - - - -
480A PHE* 1.3 73.3 - - - +
482A ASP* 1.3 60.8 + - - +
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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
------------------------------------------------------------
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