Contacts of the strand formed by residues 452 - 459 (chain A) in PDB entry 4EEP
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 452 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A LYS* 3.6 37.0 - - + +
442A ILE* 4.4 14.4 - - + +
445A ALA* 3.9 19.3 - - + -
450A ARG* 5.3 7.6 - - - +
451A GLU* 1.3 76.3 - - - +
453A THR* 1.3 67.9 + - - +
454A VAL* 3.8 27.4 - - + -
470A PHE* 3.8 1.5 - - + +
471A HIS* 3.4 2.9 + - - -
472A LEU* 2.9 48.4 + - + +
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Residues in contact with THR 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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451A GLU* 5.4 0.3 + - - -
452A ILE* 1.3 73.3 - - - +
454A VAL* 1.3 67.8 + - - +
469A LEU 6.1 0.4 - - - -
470A PHE 3.3 10.8 - - - +
471A HIS* 2.7 33.8 + - + +
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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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438A THR* 3.8 26.7 - - + -
441A LYS* 4.8 12.3 - - + -
442A ILE* 3.9 24.2 - - + -
452A ILE* 3.8 28.0 - - + -
453A THR* 1.3 82.4 - - - +
455A GLN* 1.3 65.8 + - - +
456A LEU* 4.3 2.7 - - + -
468A ASN 3.8 0.2 - - - +
469A LEU* 3.7 0.5 - - - -
470A PHE* 2.8 50.8 + - + -
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Residues in contact with GLN 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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438A THR* 3.6 14.3 + - - +
454A VAL* 1.3 78.1 - - - +
456A LEU* 1.3 63.6 + - - +
467A TRP* 3.8 26.2 - - + -
468A ASN 3.4 6.7 - - - +
469A LEU* 3.7 27.0 - - + +
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Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A GLN* 4.5 0.2 - - - +
434A THR* 3.9 22.7 - - + -
435A ASP* 5.5 3.6 - - + +
438A THR* 3.9 14.4 - - + -
439A VAL* 4.4 10.1 - - + -
442A ILE* 3.9 25.8 - - + -
454A VAL* 4.6 2.0 - - + -
455A GLN* 1.3 77.0 - - - +
457A ILE* 1.3 62.5 + - - +
458A ASN* 3.9 7.0 - - - +
467A TRP* 3.7 11.0 - - - -
468A ASN* 2.8 52.9 + - + +
470A PHE* 4.0 22.2 - - + -
1001A FMN 3.5 23.6 - - + +
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Residues in contact with ILE 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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433A GLU* 3.7 28.0 - - + +
434A THR* 2.7 31.2 + - - +
435A ASP 5.2 1.6 - - - +
456A LEU* 1.3 72.3 - - - +
458A ASN* 1.3 65.6 + - - +
459A TYR* 3.6 22.9 - - + +
465A LYS* 3.6 41.7 - - + +
466A PHE 3.6 8.1 - - - +
467A TRP* 3.5 50.2 - - + +
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Residues in contact with ASN 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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429A LEU* 3.3 28.8 - - + +
430A GLN* 3.9 2.4 - - - +
456A LEU* 3.4 4.7 + - - +
457A ILE* 1.3 82.9 - - - +
459A TYR* 1.3 65.1 + - - +
465A LYS* 3.4 6.1 - - - +
466A PHE* 2.8 57.4 + - + +
468A ASN* 2.9 23.5 - - + +
1001A FMN 2.8 44.3 + - - +
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Residues in contact with TYR 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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416A TYR* 4.7 1.7 + - - -
428A PHE 5.0 1.4 - - - +
429A LEU* 2.8 36.9 + - - +
430A GLN 3.8 2.0 - - - +
431A GLY* 3.4 39.3 - - - -
432A PRO* 3.6 15.5 - - + +
433A GLU* 2.9 36.6 + - - +
434A THR* 4.0 0.7 - - - -
457A ILE* 3.6 20.5 - - + +
458A ASN* 1.3 76.7 - - - +
460A THR* 1.3 69.3 + - - +
463A GLY* 3.7 24.0 - - - -
464A LYS 3.3 4.0 - - - +
465A LYS* 3.7 24.2 - - + +
466A PHE* 3.8 4.5 - - - -
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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