Contacts of the strand formed by residues 467 - 478 (chain A) in PDB entry 4U7C
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 VAL 467 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A LYS* 3.9 20.9 - - + -
460A LEU 3.3 7.2 - - - +
461A LYS* 3.6 33.4 - - + -
465A PHE 3.5 6.7 + - - +
466A GLU* 1.3 74.9 - - - +
468A LYS* 1.3 72.1 + - - +
469A THR* 4.8 3.8 - - + -
603A PEG 3.6 45.5 - - - +
8C G 4.6 7.8 + - - +
9C A 5.1 6.4 + - - -
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Residues in contact with LYS 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ILE 4.1 0.3 - - - +
459A LYS* 3.7 1.2 - - - -
460A LEU* 2.9 51.6 + - + +
462A ASN* 6.1 2.5 - - - +
466A GLU* 5.3 3.6 - - - +
467A VAL* 1.3 78.9 - - - +
469A THR* 1.3 65.1 + - - +
470A ARG* 3.6 25.4 - - + +
495A GLU* 3.8 21.0 + - + +
504A LEU* 6.2 2.0 - - - +
8C G 3.6 20.6 - - - +
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Residues in contact with THR 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A THR* 3.8 14.6 - - + +
458A ILE 3.2 12.6 - - - +
459A LYS* 4.1 22.7 - - + -
467A VAL* 4.8 4.9 - - + -
468A LYS* 1.3 78.3 - - - +
470A ARG* 1.3 84.9 + - - +
603A PEG 5.9 2.0 - - - +
7C G 3.7 21.2 + - - +
8C G 3.1 21.3 + - + +
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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
----------------------------------------------------------
457A THR* 3.3 1.9 - - - -
458A ILE* 2.9 41.4 + - + -
460A LEU* 5.6 1.3 - - + -
468A LYS* 3.6 33.3 - - + +
469A THR* 1.3 89.2 + - - +
471A ALA* 1.3 61.0 + - - +
491A LEU* 3.6 24.8 - - + +
495A GLU* 2.9 42.6 + - + +
7C G 3.4 32.4 + - - +
8C G 3.3 22.4 + - - -
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Residues in contact with ALA 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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455A THR* 4.3 5.8 - - + -
456A VAL 3.2 5.4 - - - +
457A THR* 3.5 23.1 - - + +
470A ARG* 1.3 75.0 - - - +
472A SER* 1.3 70.0 + - - +
491A LEU* 3.6 6.7 - - - +
6C C 3.9 28.4 + - + +
7C G 2.7 22.5 + - - +
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Residues in contact with SER 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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454A ARG 3.6 1.0 - - - +
455A THR* 3.3 2.1 - - - -
456A VAL* 2.9 31.7 + - - +
471A ALA* 1.3 81.1 + - - +
473A THR* 1.3 63.8 + - - +
474A VAL* 4.5 7.0 - - - +
487A ILE* 3.6 26.3 - - - +
490A GLU* 5.9 1.4 - - - +
491A LEU* 3.3 17.7 - - - +
6C C 3.4 5.2 - - - -
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Residues in contact with THR 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ARG* 3.2 37.0 - - - +
455A THR* 2.8 22.5 + - - +
472A SER* 1.3 75.5 - - - +
474A VAL* 1.3 65.9 + - - +
515A SER* 4.9 0.4 - - - +
5C G 3.4 24.3 + - - +
6C C 2.7 29.6 + - - -
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Residues in contact with VAL 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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454A ARG* 2.8 40.4 + - + +
472A SER* 4.5 8.7 - - - +
473A THR* 1.3 81.3 - - - +
475A SER* 1.3 66.7 + - - +
476A SER 3.2 22.0 - - - +
478A VAL* 4.4 14.6 - - + -
487A ILE* 3.8 26.9 - - + -
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Residues in contact with SER 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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454A ARG* 3.9 11.7 + - - +
474A VAL* 1.3 77.3 - - - +
476A SER* 1.3 66.7 + - - +
477A VAL* 5.7 0.2 - - - +
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Residues in contact with SER 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ARG* 3.8 2.6 - - - +
474A VAL* 3.2 23.3 - - - +
475A SER* 1.3 82.7 - - - +
477A VAL* 1.3 71.1 + - - +
478A VAL* 4.1 1.7 - - - +
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Residues in contact with VAL 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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452A LYS* 3.7 51.9 - - + +
453A GLY* 3.5 9.6 - - - +
454A ARG* 4.0 19.3 - - + -
476A SER* 1.3 82.2 - - - +
478A VAL* 1.3 63.3 + - - +
483A GLU* 5.4 1.2 - - - +
515A SER 5.1 0.2 - - - +
517A PRO* 4.7 14.8 - - + -
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Residues in contact with VAL 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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451A LEU 4.6 0.2 - - - +
452A LYS* 3.6 2.9 - - - -
453A GLY 2.6 36.2 + - - +
454A ARG* 5.1 0.4 - - - -
456A VAL* 4.9 3.1 - - + -
474A VAL* 4.4 13.5 - - + -
476A SER 4.1 7.9 - - - +
477A VAL* 1.3 78.9 - - - +
479A SER* 1.3 66.0 + - - +
483A GLU* 3.5 36.1 - - + +
484A ILE* 3.6 25.6 - - + +
487A ILE* 4.6 13.7 - - + -
513A ILE* 3.8 9.3 - - + +
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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