Contacts of the strand formed by residues 480 - 486 (chain D) in PDB entry 3F7F
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 ASN 480 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA 3.3 3.9 - - - +
10D ASN* 2.7 25.2 + - - +
71D HIS* 5.6 0.9 + - - -
418D GLN* 3.1 22.7 + - - +
419D ILE* 4.6 3.3 - - - +
457D PHE* 3.7 20.1 - - - +
458D ASN* 4.3 9.7 + - - +
475D CYS* 3.1 34.5 + - + +
477D GLN* 3.2 31.1 + - - +
478D PRO 3.2 5.9 + - - -
479D TYR* 1.3 77.7 - - - +
481D HIS* 1.3 67.4 + - - +
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Residues in contact with HIS 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASP* 3.9 1.0 - - - +
9D ALA* 2.7 39.7 + - + +
11D LEU* 3.6 28.5 - - + +
58D ASN 5.9 0.2 - - - -
59D CYS* 4.1 0.7 - - - -
69D CYS* 3.4 28.4 - - + -
71D HIS* 5.3 4.3 - - - -
82D TYR* 2.8 24.1 + - - -
84D LEU* 3.9 11.8 - - + +
458D ASN* 5.0 1.2 - - - +
472D LEU* 4.2 13.3 - - + +
473D VAL 3.4 8.7 - - - +
474D ASN* 3.1 32.1 + - + -
475D CYS* 3.8 3.9 - - - -
479D TYR 4.0 0.4 - - - -
480D ASN* 1.3 83.1 + - - +
482D SER* 1.3 66.2 + - - +
483D LEU 4.3 0.4 - - - -
610D PHE* 4.8 2.7 - - + -
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Residues in contact with SER 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ARG* 3.5 20.3 + - - -
7D ILE 3.6 3.8 - - - -
8D ASP* 2.5 26.8 + - - -
458D ASN* 3.7 4.7 + - - -
472D LEU* 3.7 4.4 - - - -
473D VAL* 2.8 50.1 + - - +
475D CYS* 4.2 5.4 - - - -
481D HIS* 1.3 75.8 + - - +
483D LEU* 1.3 61.5 + - - +
484D TYR* 3.8 10.2 + - - -
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Residues in contact with LEU 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ARG* 3.7 1.4 - - - -
7D ILE* 2.8 49.5 + - + +
466D TYR* 6.0 0.2 - - + -
470D ILE* 3.4 26.0 - - + -
471D ILE 3.9 10.3 - - - +
472D LEU* 4.1 8.4 - - + +
481D HIS 4.3 0.4 - - - -
482D SER* 1.3 72.1 - - - +
484D TYR* 1.3 65.0 + - - +
485D LYS* 3.5 33.4 + - + +
610D PHE* 4.4 12.6 - - + -
614D ILE* 3.8 41.1 - - + +
692D PHE* 4.7 8.3 - - + -
698D LEU* 4.4 8.5 - - + -
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Residues in contact with TYR 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.1 9.0 - - + +
5D SER 3.2 13.7 - - - -
6D ARG* 3.5 25.4 + - + -
354D LEU* 5.4 1.0 - - + +
361D SER* 3.6 19.4 + - - -
363D LEU* 3.8 25.5 - - + +
381D SER* 3.8 20.4 - - - -
382D VAL 3.5 22.0 - - - -
383D ASN* 3.7 11.9 + - - -
471D ILE* 3.2 25.2 + - + +
473D VAL* 3.8 26.7 - - + -
482D SER* 3.8 22.7 - - - -
483D LEU* 1.3 73.3 - - - +
485D LYS* 1.3 58.1 + - - +
695D TYR* 2.7 30.1 + - - -
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Residues in contact with LYS 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.3 2.8 - - - -
5D SER* 2.7 43.2 + - - +
7D ILE* 4.0 9.9 - - + -
483D LEU* 3.5 16.7 + - + +
484D TYR* 1.3 73.1 - - - +
486D LEU* 1.3 84.3 + - - +
488D THR* 4.1 9.5 - - - +
491D GLU* 2.6 34.2 + - - -
618D SER* 4.0 25.1 - - - +
621D GLN* 3.6 20.4 - - - +
695D TYR* 3.9 3.4 - - + -
698D LEU* 3.7 28.3 - - + -
699D ILE* 4.5 8.0 - - + +
702D ILE* 5.4 6.0 - - + +
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Residues in contact with LEU 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D CYS* 3.8 14.8 - - + +
4D LEU* 4.2 8.2 - - + +
340D LEU* 4.7 7.6 - - + -
341D GLU* 3.7 50.0 - - + +
342D LEU* 4.4 21.1 - - + -
343D ASN* 5.3 2.7 - - - +
484D TYR 4.0 0.4 + - - -
485D LYS* 1.3 93.5 + - - +
487D ASN* 1.3 70.5 + - - +
488D THR 3.9 0.2 + - - -
695D TYR* 3.6 38.7 - - + -
699D ILE* 4.0 16.8 - - + +
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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