Contacts of the strand formed by residues 478 - 484 (chain A) in PDB entry 2F61
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 GLY 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ILE* 3.4 9.8 - - - +
57A GLN 3.4 9.4 - - - -
58A ALA* 4.5 3.6 - - - -
472A ILE 3.7 0.5 - - - +
473A LYS* 3.4 5.9 - - - +
474A ASP 2.9 33.8 + - - +
475A PRO 4.9 0.8 + - - -
477A VAL* 1.3 77.6 - - - +
479A PHE* 1.3 70.6 + - - -
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Residues in contact with PHE 479 (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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55A PRO 4.1 0.9 - - - +
56A ILE* 3.4 4.4 - - - +
57A GLN* 2.5 45.8 + - - +
58A ALA* 3.6 22.7 - - - -
59A ASN 3.6 13.2 - - - +
60A HIS* 3.6 39.9 - + + -
66A LEU* 4.5 4.7 - - + -
471A THR* 3.9 17.7 - - + -
472A ILE 3.4 3.6 - - - -
473A LYS* 3.6 44.0 - - + -
478A GLY* 1.3 79.3 - - - -
480A LEU* 1.3 61.4 + - - +
481A GLU* 3.7 6.3 + - - +
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Residues in contact with LEU 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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37A PHE* 3.3 59.0 - - + -
55A PRO 4.4 4.0 - - - -
56A ILE* 4.2 9.8 - - + +
470A LEU 3.8 0.7 - - - +
471A THR* 3.4 4.0 - - - -
472A ILE* 2.6 46.8 + - + +
478A GLY 4.1 0.2 + - - -
479A PHE* 1.3 71.8 - - - +
481A GLU* 1.3 66.0 + - - +
482A THR* 3.6 22.7 + - + +
492A TYR* 3.9 21.1 - - + -
494A TRP* 4.0 23.6 - - + -
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Residues in contact with GLU 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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37A PHE* 4.9 4.9 - - - -
39A ARG* 4.6 4.2 + - - -
55A PRO 4.8 3.6 + - - -
57A GLN* 5.2 11.2 - - - +
59A ASN 5.0 4.3 - - - +
60A HIS* 3.0 14.9 - - - -
61A THR* 2.9 30.8 + - + +
62A GLY* 2.8 30.8 + - - -
470A LEU 4.0 2.8 - - - +
471A THR* 2.6 26.9 + - - +
479A PHE* 3.7 7.0 + - - +
480A LEU* 1.3 72.6 - - - +
482A THR* 1.3 64.1 + - - +
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Residues in contact with THR 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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39A ARG* 2.7 29.0 + - - +
469A PRO* 4.1 0.9 - - - +
470A LEU* 2.9 54.7 + - + +
472A ILE* 4.9 2.5 - - + -
480A LEU* 3.9 13.0 - - + +
481A GLU* 1.3 78.3 + - - +
483A ILE* 1.3 80.2 + - - +
492A TYR* 2.9 28.9 + - + +
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Residues in contact with ILE 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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467A ASP* 4.2 20.4 - - + +
468A VAL 3.7 10.5 - - - +
469A PRO* 4.5 12.3 - - + -
470A LEU 4.4 0.2 - - - +
482A THR* 1.3 91.9 + - - +
484A SER* 1.3 71.1 + - - +
485A PRO* 3.0 21.9 - - + +
490A HIS* 3.5 13.9 - - - -
492A TYR* 5.0 0.2 - - - -
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Residues in contact with SER 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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444A LEU* 3.7 20.3 - - - +
460A VAL* 4.0 16.4 + - - +
462A ASN* 2.8 49.6 + - - +
468A VAL 2.8 30.8 + - - -
470A LEU* 4.8 6.6 - - - +
483A ILE* 1.3 71.9 - - - +
485A PRO* 1.3 58.2 - - - +
488A SER* 3.9 4.2 + - - -
490A HIS* 4.7 6.8 - - - -
492A TYR* 6.0 0.4 - - - -
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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