Contacts of the strand formed by residues 81 - 90 (chain C) in PDB entry 1PFX
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 GLN 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C VAL 3.7 1.4 - - - +
67C VAL 4.7 0.4 - - - -
68C ALA* 2.9 34.8 + - + +
79C THR 3.4 10.7 + - - +
80C GLU* 1.3 78.7 - - - +
82C ARG* 1.3 65.4 + - - +
83C ARG* 3.8 10.7 + - - +
112C LEU* 3.6 22.0 - - + +
113C THR* 2.7 56.4 + - - -
115C ASN* 3.0 17.4 - - - +
118C VAL* 3.1 12.9 - - + +
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Residues in contact with ARG 82 (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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34C ASN* 4.2 17.8 - - - +
65C THR* 5.2 11.7 + - + -
66C VAL 3.2 10.8 - - - +
67C VAL* 4.4 19.8 - - + +
70C GLU* 5.8 0.4 - - - +
76C THR* 5.6 3.0 - - - +
80C GLU* 3.5 28.0 + - + +
81C GLN* 1.3 76.3 - - - +
83C ARG* 1.3 85.3 + - - +
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Residues in contact with ARG 83 (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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65C THR* 3.0 29.1 - - - +
66C VAL* 3.1 20.9 + - + -
81C GLN* 3.8 22.6 + - - +
82C ARG* 1.3 104.1 + - - +
84C ASN* 1.3 68.9 + - - +
108C LEU* 3.6 16.4 - - + -
109C ASP* 4.1 4.3 - - - -
110C GLU* 2.7 41.7 + - - +
111C PRO 2.7 21.2 + - - -
112C LEU* 3.2 34.5 - - + +
113C THR* 3.9 7.1 + - - +
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Residues in contact with ASN 84 (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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64C ILE 3.7 4.9 - - - +
65C THR* 3.3 21.5 - - - +
83C ARG* 1.3 78.8 - - - +
85C VAL* 1.3 67.1 + - - +
86C ILE* 3.6 1.6 + - + +
108C LEU* 3.5 4.2 - - - -
109C ASP* 2.8 51.2 + - + +
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Residues in contact with VAL 85 (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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63C LYS* 6.1 0.7 - - - -
64C ILE* 3.0 48.1 + - + +
66C VAL* 4.2 10.1 - - + -
84C ASN* 1.3 74.4 - - - +
86C ILE* 1.3 59.7 + - - +
87C ARG 3.0 32.1 - - - +
88C ALA* 4.3 4.0 - - + +
106C LEU* 4.0 33.9 - - + -
107C GLU 3.8 6.5 - - - +
108C LEU* 4.7 0.9 - - + +
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Residues in contact with ILE 86 (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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50C LYS* 5.0 4.3 - - - +
84C ASN* 3.7 2.5 - - + +
85C VAL* 1.3 76.9 - - - +
87C ARG* 1.3 65.4 + - + +
107C GLU* 3.0 39.5 + - + +
108C LEU 4.9 0.2 - - - +
109C ASP* 3.3 44.4 - - + +
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Residues in contact with ARG 87 (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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51C TRP* 3.1 18.0 - - - -
85C VAL* 3.0 17.6 - - - +
86C ILE* 1.3 84.7 - - + +
88C ALA* 1.3 63.3 + - - +
89C ILE* 3.4 39.1 - - + +
105C LEU 3.8 0.6 - - - +
106C LEU* 3.6 0.3 - - - -
107C GLU* 2.9 62.9 + - + +
241C LYS* 5.6 1.4 - - - +
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Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C ILE* 3.6 36.2 - - + +
64C ILE* 6.4 0.7 - - + -
85C VAL* 4.5 4.9 - - + -
87C ARG* 1.3 76.8 - - - +
89C ILE* 1.3 60.5 + - - +
90C PRO* 3.0 14.0 - - - +
105C LEU 3.5 5.6 - - - -
106C LEU* 4.0 11.0 - - + -
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Residues in contact with ILE 89 (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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51C TRP* 4.0 20.2 - - + +
59C ILE* 4.8 0.2 - - - +
87C ARG* 3.4 51.4 - - + +
88C ALA* 1.3 71.0 - - - +
90C PRO* 1.3 75.8 - - + +
92C HIS* 5.2 4.5 - - + -
104C ALA* 3.5 1.4 - - - -
105C LEU* 3.0 34.8 + - + +
237C TRP* 3.6 8.7 - - + -
241C LYS* 3.7 37.9 - - + +
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Residues in contact with PRO 90 (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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56C ALA* 4.1 18.2 - - + +
59C ILE* 3.4 27.6 - - + -
88C ALA 3.0 18.8 - - - +
89C ILE* 1.3 90.8 - - + +
91C HIS* 1.3 69.7 + - - +
92C HIS* 3.2 5.2 + - - -
94C TYR* 4.5 9.9 - - + -
104C ALA* 3.5 10.1 - - + -
237C TRP* 4.0 0.7 - - - -
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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