Contacts of the strand formed by residues 449 - 459 (chain A) in PDB entry 2E3S
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 ILE 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A ARG* 4.6 14.1 - - + +
443A ASN* 6.0 1.6 - - - +
446A GLU* 3.4 39.6 - - + +
447A THR 3.5 2.5 - - - -
448A THR* 1.3 80.5 - - - +
450A GLU* 1.3 65.6 + - - +
451A ASN* 3.5 28.7 - - - +
452A PHE* 4.2 13.5 - - + -
467A GLN* 3.4 39.7 - - + +
468A THR 3.6 4.9 - - - +
469A HIS* 3.9 8.7 - - + +
470A LYS* 2.9 18.8 + - - -
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Residues in contact with GLU 450 (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 ILE* 1.3 75.5 - - - +
451A ASN* 1.3 82.3 + - - +
468A THR* 2.9 23.7 + - - +
469A HIS 4.2 7.4 - - - -
470A LYS* 3.8 19.5 + - + +
477A GLN* 2.7 37.9 + - - +
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Residues in contact with ASN 451 (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 ILE* 3.5 4.1 - - - +
450A GLU* 1.3 108.7 + - - +
452A PHE* 1.3 64.6 + - - +
466A TYR* 6.1 1.3 - - + -
467A GLN* 3.3 1.1 - - - +
468A THR* 2.9 37.8 + - + +
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Residues in contact with PHE 452 (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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439A VAL* 3.8 45.5 - - + -
442A ARG* 3.8 24.0 - - + -
443A ASN* 3.8 27.8 - - - -
449A ILE* 4.2 13.5 - - + -
451A ASN* 1.3 79.4 - - - +
453A HIS* 1.3 75.7 + - - +
454A VAL* 4.9 4.0 - - + -
465A ILE* 4.0 14.8 - - + -
466A TYR* 3.2 7.4 - - - +
467A GLN* 3.4 24.0 - - + +
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Residues in contact with HIS 453 (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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452A PHE* 1.3 85.4 - - - +
454A VAL* 1.3 72.8 + - - +
455A VAL* 3.4 26.7 + - + -
465A ILE* 3.5 2.1 - - - -
466A TYR* 2.9 59.3 + + + +
512A ALA* 6.2 0.7 - - + -
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Residues in contact with VAL 454 (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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439A VAL* 4.0 36.8 - - + -
452A PHE* 4.9 3.4 - - + -
453A HIS* 1.3 78.0 + - - +
455A VAL* 1.3 62.1 + - - +
456A GLU* 3.6 26.5 - - - +
457A THR* 4.0 12.1 - - - +
463A ILE* 4.1 18.6 - - + -
464A ILE 3.5 6.7 - - - +
465A ILE* 4.5 3.4 - - + +
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Residues in contact with VAL 455 (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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453A HIS* 3.6 26.0 - - + -
454A VAL* 1.3 74.2 - - - +
456A GLU* 1.3 58.5 + - + +
464A ILE* 2.7 17.9 + - + +
466A TYR* 3.7 26.9 - - + +
481A LEU* 4.0 9.2 - - + -
509A HIS* 3.5 45.0 + - + +
511A SER* 4.5 9.0 - - - -
512A ALA* 4.8 5.4 - - + -
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Residues in contact with GLU 456 (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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366A ARG* 2.8 45.4 + - - -
454A VAL* 3.4 8.1 - - - +
455A VAL* 1.3 81.5 - - + +
457A THR* 1.3 75.2 + - - +
458A LEU* 3.4 13.9 + - + +
463A ILE* 3.5 3.1 - - - -
464A ILE* 2.9 36.1 + - + +
509A HIS* 2.8 21.0 + - + -
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Residues in contact with THR 457 (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 VAL* 4.0 12.6 - - - +
456A GLU* 1.3 82.1 - - - +
458A LEU* 1.3 61.1 + - - +
459A ALA* 3.4 24.9 - - - +
460A ASP* 5.5 1.1 - - - -
462A ALA 4.1 1.6 - - - -
463A ILE* 4.0 11.7 - - + +
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Residues in contact with LEU 458 (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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365A HIS* 3.8 42.2 - - + +
366A ARG* 3.7 14.4 - - - +
367A PHE* 3.9 13.2 - - + -
456A GLU* 3.4 29.4 + - + +
457A THR* 1.3 75.2 - - - +
459A ALA* 1.3 63.2 + - - +
462A ALA* 2.9 19.7 + - + +
463A ILE* 4.8 0.7 - - - -
464A ILE* 3.9 19.1 - - + -
483A LEU* 3.6 36.8 - - + -
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Residues in contact with ALA 459 (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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365A HIS* 4.2 15.9 - - + -
457A THR* 3.4 16.8 - - - +
458A LEU* 1.3 78.4 - - - +
460A ASP* 1.3 67.7 + - - +
461A ASN* 3.1 19.5 - - - +
462A ALA* 3.0 17.1 + - + +
463A ILE* 4.8 1.0 - - - +
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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