Contacts of the strand formed by residues 64 - 69 (chain D) in PDB entry 1PXV
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 ARG 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B ASP* 6.2 0.2 - - - -
338B LEU* 6.1 1.1 - - - -
382B ARG* 3.5 19.0 - - - +
461B SO4 2.9 44.5 + - - -
23D ASN* 4.0 1.6 + - - -
27D PHE* 4.3 0.2 - - - -
58D ILE* 4.5 0.2 - - - +
59D ASP* 2.8 49.5 + - + +
62D HIS* 3.7 21.6 - - + +
63D GLN* 1.3 75.5 - - - +
65D ILE* 1.4 70.9 + - - +
66D LYS* 4.4 16.3 - - + +
78D ILE* 3.7 18.8 - - + +
79D LEU 3.1 13.0 - - - +
80D ASP* 2.6 41.6 + - - +
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Residues in contact with ILE 65 (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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9D LEU* 4.1 24.2 - - + -
23D ASN* 4.9 1.1 - - + -
24D ILE* 4.4 13.0 - - + +
27D PHE* 3.8 34.3 - - + -
55D ILE* 4.8 10.3 - - + -
57D PHE 3.4 7.2 - - - +
58D ILE* 4.0 26.2 - - + -
64D ARG* 1.4 81.3 - - - +
66D LYS* 1.3 65.5 + - - +
67D PHE* 3.9 23.2 - - + -
77D TYR 3.8 0.7 - - - +
78D ILE* 3.4 3.8 - - - +
79D LEU* 2.9 43.9 + - + +
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B SER* 4.3 6.7 + - - -
329B VAL 5.7 0.8 + - - -
330B SER* 4.6 0.6 + - - -
335B ASP* 2.7 36.9 + - - +
336B PRO* 2.9 28.8 + - + +
338B LEU* 4.0 30.5 - - + +
55D ILE* 3.7 3.1 - - - +
56D LEU* 2.7 40.3 + - + -
57D PHE* 3.0 17.7 + - + +
59D ASP* 6.5 0.7 - - + -
64D ARG* 4.4 19.5 - - + +
65D ILE* 1.3 77.6 - - - +
67D PHE* 1.3 58.8 + - - +
76D ILE* 4.2 8.5 - - + -
77D TYR 3.1 7.0 - - - +
78D ILE* 4.0 15.5 - - + -
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Residues in contact with PHE 67 (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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7D ILE* 3.9 27.4 - - + -
9D LEU* 4.0 10.8 - - + -
53D TYR* 3.6 32.8 - + + -
54D HIS 3.1 19.5 - - - +
55D ILE* 4.0 4.5 - - + -
56D LEU* 4.0 6.5 - - - +
65D ILE* 3.9 21.5 - - + -
66D LYS* 1.3 79.9 - - - +
68D SER* 1.3 65.0 + - - +
76D ILE* 3.7 0.9 - - - -
77D TYR* 2.8 64.7 + + + +
79D LEU* 3.6 39.7 - - + -
89D MET* 4.9 2.2 - - - -
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Residues in contact with SER 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D TYR* 3.2 8.1 - - - -
54D HIS* 2.8 36.7 + - - +
56D LEU* 3.4 24.9 - - - +
67D PHE* 1.3 74.9 + - - +
69D SER* 1.3 68.0 + - - +
72D ASN 4.3 4.7 - - - -
73D GLU* 4.3 11.9 + - - -
75D ILE 2.9 22.8 + - - -
76D ILE* 3.8 3.1 - - - +
77D TYR* 4.4 2.7 - - - -
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Residues in contact with SER 69 (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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52D GLN 3.7 3.8 - - - -
53D TYR* 3.5 32.6 - - - -
68D SER* 1.3 76.8 - - - +
70D PHE* 1.3 66.3 + - - +
71D ASP* 2.7 26.0 + - - -
72D ASN* 3.1 28.2 + - - +
73D GLU* 4.4 2.6 + - - +
77D TYR* 4.5 8.0 + - - -
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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