Contacts of the strand formed by residues 460 - 466 (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 ALA 460 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332D VAL* 3.9 9.9 - - + +
354D LEU* 3.9 23.8 - - + -
356D LYS* 3.2 31.4 + - + +
359D THR 5.4 1.4 + - - -
361D SER* 4.1 25.6 - - - -
458D ASN 3.1 5.4 + - - +
459D GLU* 1.3 74.3 - - - +
461D SER* 1.3 58.8 + - - +
473D VAL* 4.1 14.6 - - + -
474D ASN 4.3 0.4 - - - -
475D CYS* 4.9 0.2 - - - +
476D PHE* 3.4 3.5 - - - -
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Residues in contact with SER 461 (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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55D GLU 4.7 0.3 + - - -
56D TYR* 3.6 19.8 - - - -
57D SER* 3.0 36.6 + - - -
105D ARG* 5.4 0.9 + - - -
332D VAL* 3.3 21.8 - - - +
460D ALA* 1.3 74.9 - - - +
462D SER* 1.3 61.9 + - - +
473D VAL* 4.5 0.4 - - - +
474D ASN 3.0 19.9 + - - -
476D PHE* 3.8 20.0 - - - -
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Residues in contact with SER 462 (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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56D TYR* 4.4 4.3 - - - -
57D SER 2.8 23.7 + - - -
58D ASN* 3.4 22.4 - - - -
332D VAL* 4.1 0.8 - - - +
333D ASP* 3.7 15.5 - - - -
354D LEU* 4.3 3.9 - - - +
461D SER* 1.3 81.6 - - - +
463D ILE* 1.3 65.0 + - - +
473D VAL* 3.4 8.7 - - - +
474D ASN* 2.9 40.0 + - - +
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Residues in contact with ILE 463 (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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58D ASN* 3.9 9.7 + - - +
333D ASP* 3.1 47.8 + - + +
334D LEU 4.4 0.2 - - - -
335D VAL* 3.6 34.8 - - + -
352D ILE* 3.8 17.3 - - + +
354D LEU* 3.9 18.6 - - + -
363D LEU* 5.1 1.3 - - + -
462D SER* 1.3 79.9 - - - +
464D THR* 1.3 75.6 + - - +
465D LEU* 4.7 5.8 - - + +
471D ILE* 4.5 10.5 - - + -
472D LEU 3.3 15.3 - - - +
473D VAL* 4.9 3.8 - - + -
474D ASN* 4.1 0.2 - - - -
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Residues in contact with THR 464 (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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58D ASN* 3.6 2.1 + - - -
59D CYS* 3.1 36.4 + - + +
67D TYR* 4.1 16.4 - - + -
463D ILE* 1.3 78.4 + - - +
465D LEU* 1.3 62.2 + - - +
466D TYR 3.2 10.2 + - - +
472D LEU* 2.9 51.3 + - + +
474D ASN* 2.7 26.8 + - - -
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Residues in contact with LEU 465 (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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67D TYR* 3.4 7.6 + - - -
335D VAL* 3.5 33.4 - - + -
337D THR* 4.3 21.3 - - + +
352D ILE* 3.8 25.4 - - + -
463D ILE* 4.3 2.6 - - + -
464D THR* 1.3 73.7 - - - +
466D TYR* 1.3 65.7 + - - +
467D GLY 3.4 10.9 + - - +
468D ASP 4.8 7.0 - - - +
469D GLU* 4.2 20.2 - - - +
470D ILE 3.4 10.8 - - - +
471D ILE* 4.6 2.2 - - + -
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Residues in contact with TYR 466 (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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67D TYR* 3.4 31.6 - + - -
84D LEU* 3.4 32.3 - - + -
85D SER* 6.1 0.2 - - - -
464D THR* 3.2 5.1 + - - -
465D LEU* 1.3 70.6 - - - +
467D GLY* 1.3 63.4 + - - +
470D ILE* 2.9 60.7 + - + +
472D LEU* 4.2 16.6 - - + -
608D ASP* 4.1 9.0 + - - -
610D PHE* 3.6 22.6 - + + +
611D THR* 3.6 19.5 - - + +
691D LYS* 5.4 4.0 - - - +
692D PHE* 3.8 34.5 + + - -
693D PHE* 5.6 5.5 - + - -
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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