Contacts of the strand formed by residues 64 - 69 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A ASN 5.1 0.6 + - - -
382A ARG* 3.5 22.9 - - - +
462A SO4 3.1 40.3 + - - -
23C ASN* 3.2 9.0 + - - +
27C PHE* 4.1 1.3 - - - -
59C ASP* 2.7 64.0 + - + +
62C HIS* 4.0 17.3 + - - +
63C GLN* 1.3 77.8 - - - +
65C ILE* 1.3 67.7 + - - +
66C LYS* 4.5 15.3 - - + +
78C ILE* 3.5 20.9 - - + +
79C LEU 3.1 15.0 - - - +
80C ASP* 2.8 35.3 + - - +
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Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 4.2 25.1 - - + -
23C ASN* 4.0 8.7 - - - +
24C ILE* 4.4 14.6 - - + -
27C PHE* 3.7 28.0 - - + -
55C ILE* 5.1 10.3 - - + -
57C PHE 3.4 9.0 - - - +
58C ILE* 4.4 10.5 - - + -
64C ARG* 1.3 81.9 - - - +
66C LYS* 1.3 61.2 + - - +
67C PHE* 3.8 26.8 - - + -
77C TYR 3.9 0.3 - - - +
78C ILE* 3.5 2.6 - - - -
79C LEU* 2.9 49.3 + - + +
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Residues in contact with LYS 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A SER* 4.8 3.2 + - - -
330A SER* 6.1 0.2 - - - +
335A ASP* 2.6 30.8 + - - +
336A PRO* 2.8 38.0 + - + -
337A HIS* 4.8 1.8 - - - +
338A LEU* 4.2 14.0 - - - +
55C ILE* 3.7 3.3 - - - +
56C LEU* 2.8 30.1 + - + -
57C PHE* 3.0 26.0 + - + +
64C ARG* 4.5 15.9 - - + +
65C ILE* 1.3 75.4 - - - +
67C PHE* 1.3 64.0 + - - +
76C ILE* 4.5 7.2 - - + -
77C TYR 3.2 6.1 - - - +
78C ILE* 3.9 33.4 - - + -
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Residues in contact with PHE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 4.0 26.5 - - + -
9C LEU* 4.1 10.3 - - + -
53C TYR* 3.6 31.9 - + + -
54C HIS 3.1 19.7 - - - +
55C ILE* 4.0 4.9 - - + -
56C LEU* 4.0 6.6 - - - +
65C ILE* 3.8 20.2 - - + -
66C LYS* 1.3 78.9 - - - +
68C SER* 1.3 61.6 + - - +
76C ILE* 3.7 1.0 - - - -
77C TYR* 2.8 69.3 + + + +
79C LEU* 3.5 39.5 - - + -
89C MET* 4.7 1.8 - - - -
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Residues in contact with SER 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TYR* 3.3 7.0 - - - -
54C HIS* 2.7 36.7 + - - +
56C LEU* 3.5 21.9 - - - +
67C PHE* 1.3 72.9 + - - +
69C SER* 1.3 69.4 + - - +
72C ASN 4.1 5.4 - - - -
73C GLU* 4.2 11.7 + - - -
75C ILE 2.9 25.6 + - - -
76C ILE* 3.8 4.2 - - - +
77C TYR* 4.3 2.9 - - - -
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Residues in contact with SER 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C GLN 3.8 4.7 - - - -
53C TYR* 3.5 32.5 - - - -
54C HIS* 5.5 0.7 - - - -
68C SER* 1.3 78.4 - - - +
70C PHE* 1.3 64.7 + - - +
71C ASP* 2.9 25.5 + - - -
72C ASN* 3.1 29.5 + - - +
73C GLU* 4.2 1.7 + - - +
75C ILE* 6.0 0.3 - - - +
77C TYR* 4.4 8.6 + - - -
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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