Contacts of the strand formed by residues 465 - 476 (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 LYS 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A GLU* 4.5 14.4 - - + +
457A ILE* 3.6 45.0 - - + +
458A ASN 3.4 4.7 - - - -
459A TYR* 3.7 23.6 - - + +
463A GLY 3.4 4.4 + - - +
464A LYS* 1.3 77.2 - - - +
466A PHE* 1.3 63.3 + - - +
467A TRP* 5.9 1.3 - - - +
493A SER* 4.8 1.4 + - - -
495A HIS* 4.8 7.6 - - - -
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Residues in contact with PHE 466 (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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413A LEU* 4.1 29.8 - - + -
414A THR* 5.0 7.9 - - + -
429A LEU* 5.2 3.4 - - + -
457A ILE* 3.6 7.7 - - - -
458A ASN* 2.8 64.2 + - + +
459A TYR 3.8 11.0 - - - -
460A THR* 3.8 23.1 - - + -
464A LYS 3.8 10.5 - - - -
465A LYS* 1.3 75.8 - - - +
467A TRP* 1.3 70.4 + - - +
468A ASN* 3.5 25.5 + - + -
491A ASP* 3.6 32.5 - - - +
493A SER* 3.7 7.2 - - - +
495A HIS* 4.7 3.4 - - + -
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Residues in contact with TRP 467 (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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435A ASP* 6.5 1.1 - - + -
455A GLN* 3.8 26.5 - - + -
456A LEU* 3.7 39.5 - - - -
457A ILE* 3.5 27.9 - - + +
465A LYS* 5.9 1.2 - - - +
466A PHE* 1.3 75.0 - - - +
468A ASN* 1.3 59.1 + - - +
469A LEU* 3.8 5.4 - - + -
490A LEU 3.4 1.4 - - - +
491A ASP* 3.6 0.2 - - - -
492A GLY* 2.7 44.3 + - - +
493A SER* 3.0 21.7 + - - +
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Residues in contact with ASN 468 (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* 4.7 1.0 - - - +
455A GLN* 3.4 3.2 - - - -
456A LEU* 2.8 44.1 + - + +
458A ASN* 2.9 30.9 - - - +
466A PHE* 3.5 16.5 + - + -
467A TRP* 1.3 69.6 - - - +
469A LEU* 1.3 77.4 + - - +
470A PHE* 3.4 9.5 + - - +
489A GLN* 3.3 25.1 - - - +
490A LEU 3.5 4.0 + - - -
1001A FMN 3.0 23.4 + - - -
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Residues in contact with LEU 469 (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 THR* 6.1 1.1 - - + -
454A VAL 3.8 4.7 - - - +
455A GLN* 3.7 31.4 - - + +
467A TRP* 4.8 6.1 - - + +
468A ASN* 1.3 71.3 - - - +
470A PHE* 1.3 59.6 + - - +
488A VAL 3.5 5.0 - - - +
489A GLN 3.6 0.2 - - - -
490A LEU* 2.8 60.1 + - + +
491A ASP 4.8 0.7 - - - +
492A GLY* 3.8 26.5 - - - +
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Residues in contact with PHE 470 (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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442A ILE* 3.9 39.3 - - + -
452A ILE* 3.8 1.9 - - + +
453A THR* 3.3 5.6 - - - +
454A VAL* 2.8 49.4 + - + +
456A LEU* 4.0 16.8 - - + -
468A ASN* 3.8 7.0 - - - +
469A LEU* 1.3 73.8 - - - +
471A HIS* 1.3 66.1 + - - +
472A LEU* 3.9 28.9 - - + -
487A GLY* 3.7 17.7 - - - -
488A VAL 3.4 8.3 - - - -
489A GLN* 4.0 5.8 - - + -
1001A FMN 3.2 55.0 - + - -
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Residues in contact with HIS 471 (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* 3.8 23.3 - - + -
452A ILE 3.4 4.0 + - - -
453A THR* 2.7 31.1 + - + +
469A LEU 4.2 0.2 + - - -
470A PHE* 1.3 76.1 - - - +
472A LEU* 1.3 74.4 + - - +
473A GLN* 3.2 28.7 + - + -
486A ILE* 3.7 2.5 - - + +
487A GLY* 3.5 2.8 - - - -
488A VAL* 2.8 58.0 + - + +
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Residues in contact with LEU 472 (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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442A ILE* 4.5 3.8 - - + +
445A ALA* 4.1 6.3 - - + -
446A ILE* 3.6 25.8 - - + +
450A ARG 4.0 18.6 - - - +
451A GLU* 3.2 24.3 - - - +
452A ILE* 2.9 31.6 + - + +
470A PHE* 3.9 12.5 - - + -
471A HIS* 1.3 77.6 + - - +
473A GLN* 1.3 66.1 + - - +
485A PHE* 3.7 26.2 - - + -
486A ILE 3.6 8.5 - - - +
1001A FMN 3.8 32.1 - - + -
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Residues in contact with GLN 473 (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* 3.3 21.4 + - - +
471A HIS* 3.2 25.4 + - + +
472A LEU* 1.3 74.9 - - - +
474A PRO* 1.3 83.0 - - + +
475A MET* 5.4 2.0 - - + +
485A PHE* 3.5 4.7 - - - -
486A ILE* 2.9 53.3 + - + +
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Residues in contact with PRO 474 (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 GLN* 3.4 27.4 - - + +
450A ARG* 3.8 5.4 - - - +
451A GLU* 3.7 20.0 - - + +
472A LEU 4.6 0.2 - - - -
473A GLN* 1.3 100.2 - - + +
475A MET* 1.3 60.1 + - - +
476A ARG* 4.1 9.3 + - + +
482A LEU* 3.7 19.5 - - + -
484A TYR 3.8 0.4 - - - +
485A PHE* 3.7 21.3 - - + -
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Residues in contact with MET 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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393A ILE* 4.2 11.9 - - + -
473A GLN* 4.1 7.0 - - + +
474A PRO* 1.3 77.8 - - - +
476A ARG* 1.3 63.0 + - - +
482A LEU* 3.8 1.3 - - - +
483A GLN* 2.8 26.7 + - + +
484A TYR* 2.8 49.1 + - + +
485A PHE 4.2 0.4 - - - -
486A ILE* 3.7 40.4 - - + -
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Residues in contact with ARG 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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448A ASP 5.0 1.0 + - - -
449A GLN* 2.6 50.5 + - - +
474A PRO* 4.3 7.1 + - + +
475A MET* 1.3 79.1 - - - +
477A ASP* 1.3 70.1 + - - +
480A GLY* 2.9 30.3 + - - -
481A GLU* 3.4 8.6 - - - +
482A LEU* 3.4 22.7 - - + +
483A GLN* 4.6 4.3 - - - +
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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