Contacts of the helix formed by residues 474 - 485 (chain A) in PDB entry 3E2E
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 PRO 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A LYS 4.5 1.3 - - - +
473A VAL* 1.4 92.6 - - + +
475A PHE* 1.3 60.2 + - - +
476A PRO* 3.4 10.5 - - + -
477A GLU* 2.9 35.5 + - + +
478A ARG 3.1 9.2 + - - -
565A GLU* 3.5 25.6 - - + +
566A THR* 4.7 3.8 - - - +
567A VAL* 3.7 8.0 - - + +
880A PHE* 3.7 15.9 - - + -
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Residues in contact with PHE 475 (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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458A TYR* 3.3 23.3 - + - +
459A TRP* 4.9 6.3 - + - -
462A ILE* 3.6 28.7 - - + -
473A VAL 3.7 0.6 + - - -
474A PRO* 1.3 69.6 - - - +
476A PRO* 1.4 71.0 - - + +
478A ARG* 2.9 42.5 + - - +
479A ILE* 3.1 17.7 + - - +
825A PHE* 4.2 12.3 - + - -
879A ASP* 3.3 51.8 - - + -
880A PHE* 3.7 15.0 - + - -
882A PHE* 3.6 20.2 - + - -
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Residues in contact with PRO 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A TYR* 4.8 3.3 - - + +
474A PRO* 3.5 11.7 - - + -
475A PHE* 1.4 95.4 - - + +
477A GLU* 1.3 54.3 - - - +
479A ILE* 3.7 10.1 - - + +
480A LYS* 3.3 22.2 + - - +
880A PHE* 6.2 0.2 - - + -
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Residues in contact with GLU 477 (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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470A VAL* 5.3 0.2 - - - +
473A VAL* 3.4 28.8 - - + +
474A PRO* 2.9 25.7 + - + +
476A PRO* 1.3 76.3 - - - +
478A ARG* 1.3 60.8 + - - +
479A ILE 3.3 0.2 - - - -
480A LYS* 3.3 11.2 + - + +
481A PHE* 3.0 26.2 + - - +
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Residues in contact with ARG 478 (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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461A LYS 5.2 0.2 - - - -
462A ILE* 3.9 13.8 - - + +
465A ALA* 3.7 18.6 - - + +
466A ASN* 2.7 32.4 + - - +
470A VAL* 4.1 16.2 + - + +
471A ASP 3.2 24.8 + - - -
473A VAL* 2.5 35.4 + - + +
474A PRO 3.1 4.4 + - - +
475A PHE* 2.9 29.9 + - - +
477A GLU* 1.3 75.8 - - - +
479A ILE* 1.3 65.2 - - - +
481A PHE* 3.2 15.8 + - - +
482A ILE* 3.3 19.8 + - - +
567A VAL* 4.4 1.8 - - - +
880A PHE* 3.8 21.4 - - - +
882A PHE* 3.2 28.3 - - - -
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Residues in contact with ILE 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A TYR* 3.6 49.8 - - + +
461A LYS* 3.7 26.7 - - + +
462A ILE* 3.6 13.5 - - + -
475A PHE 3.1 14.1 + - - +
476A PRO* 3.7 10.8 - - + +
478A ARG* 1.3 76.5 - - - +
480A LYS* 1.3 56.9 + - - +
482A ILE* 3.2 7.5 + - - +
483A GLU* 3.0 55.0 + - + +
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Residues in contact with LYS 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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476A PRO 3.3 12.9 + - - +
477A GLU* 3.4 16.8 - - + +
478A ARG 3.2 0.6 - - - -
479A ILE* 1.3 80.2 - - - +
481A PHE* 1.3 57.2 + - - +
483A GLU* 4.6 16.3 + - + +
484A GLU* 3.1 61.7 + - - +
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Residues in contact with PHE 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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465A ALA* 4.9 2.7 - - - -
468A ALA* 4.3 17.5 - - + -
470A VAL* 3.8 39.0 - - + -
477A GLU 3.0 12.8 + - - +
478A ARG* 3.4 11.7 - - - +
479A ILE 3.2 0.4 - - - -
480A LYS* 1.3 74.1 - - - +
482A ILE* 1.3 80.3 + - + +
484A GLU* 3.5 12.7 + - - +
485A ASN* 3.2 49.4 + - + -
501A TRP* 4.6 14.1 - + - -
505A GLN* 5.0 2.9 - - - -
511A PHE* 5.3 2.9 - + - -
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Residues in contact with ILE 482 (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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461A LYS* 3.4 39.7 - - + +
464A GLY 4.1 2.0 - - - -
465A ALA* 3.7 20.2 - - + +
478A ARG 3.3 13.7 - - - +
479A ILE 3.2 6.2 + - - +
481A PHE* 1.3 84.8 - - + +
483A GLU* 1.3 60.2 + - - +
485A ASN* 2.9 20.5 + - - -
486A HIS* 3.1 11.4 + - - +
489A ILE* 3.8 20.9 - - + +
511A PHE* 5.1 2.5 - - + -
514A PHE* 4.0 16.8 - - + -
518A TYR* 3.8 29.8 - - + +
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Residues in contact with GLU 483 (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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461A LYS* 3.4 18.2 + - + +
479A ILE* 3.0 41.7 + - + +
480A LYS* 4.2 19.3 + - + +
482A ILE* 1.3 76.8 - - + +
484A GLU* 1.3 61.7 + - - +
486A HIS* 3.6 18.9 - - - +
487A GLU* 5.0 0.9 - - - +
518A TYR* 5.1 6.7 - - - +
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Residues in contact with GLU 484 (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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480A LYS* 3.1 52.2 + - - +
481A PHE* 3.7 15.4 - - - +
482A ILE 3.2 0.2 - - - -
483A GLU* 1.3 78.2 - - - +
485A ASN* 1.3 66.9 + - - +
486A HIS 3.3 2.8 + - - -
487A GLU* 4.4 7.1 - - - +
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Residues in contact with ASN 485 (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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481A PHE* 3.2 38.8 + - + +
482A ILE* 2.9 10.0 + - - +
484A GLU* 1.3 86.5 - - - +
486A HIS* 1.3 56.2 + - - +
487A GLU 3.2 3.1 - - - +
488A ASN* 3.1 27.2 + - + +
489A ILE* 2.8 33.4 + - + +
501A TRP* 3.4 31.5 - - + -
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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