Contacts of the strand formed by residues 71 - 77 (chain C) in PDB entry 1XPM
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 ILE 71 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C ILE* 3.6 32.8 - - + -
67C ASP* 3.0 27.0 + - + +
68C LYS 4.3 0.6 + - - -
69C LYS 3.6 1.2 - - - -
70C LYS* 1.3 75.3 - - - +
72C GLY* 1.3 57.6 + - - +
73C MET 3.4 27.8 - - - +
74C VAL* 4.1 8.3 - - + -
98C ILE* 3.9 35.3 - - + +
99C GLN* 2.8 25.2 + - - +
102C ALA* 3.8 4.6 - - + +
132C LYS* 3.3 22.0 - - + +
133C VAL 5.1 0.2 - - - -
134C LEU* 4.1 13.0 - - + +
161C VAL* 5.5 2.2 - - + -
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Residues in contact with GLY 72 (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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70C LYS 3.3 3.8 + - - -
71C ILE* 1.3 72.8 - - - +
73C MET* 1.3 68.6 + - - +
99C GLN* 4.2 4.7 - - - -
101C PHE 4.3 3.2 - - - +
102C ALA* 3.2 11.5 - - - -
103C ARG* 3.0 19.8 + - - +
124C TYR* 4.1 7.0 + - - -
131C GLU* 3.6 21.5 + - - -
132C LYS 2.9 10.8 + - - -
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Residues in contact with MET 73 (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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71C ILE* 3.4 6.0 - - - +
72C GLY* 1.3 84.1 - - - +
74C VAL* 1.3 63.4 + - - +
75C ILE* 4.0 22.9 - - + -
102C ALA* 4.5 0.7 - - - -
103C ARG* 3.2 45.8 - - + +
105C PHE* 4.2 13.7 - - - -
121C ALA* 4.1 7.0 - - - +
124C TYR* 3.6 43.3 - - + -
132C LYS 4.1 2.8 + - - -
133C VAL* 3.6 17.1 - - + +
134C LEU 3.0 24.9 + - - -
120D LEU* 4.0 13.0 - - + -
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Residues in contact with VAL 74 (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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71C ILE* 4.1 6.1 - - + -
73C MET* 1.3 77.3 - - - +
75C ILE* 1.3 64.7 + - - +
76C VAL* 4.8 2.9 - - + -
89C ALA* 3.4 26.8 - - + +
92C ILE* 4.8 10.3 - - + -
93C HIS* 4.0 20.4 - - + +
98C ILE* 3.8 27.6 - - + -
102C ALA* 5.3 1.1 - - + -
103C ARG 2.9 7.1 + - - +
104C CYS* 3.3 14.4 - - - -
105C PHE* 3.2 22.2 + - - -
134C LEU* 3.4 22.2 - - + +
136C ILE* 4.9 2.0 - - + -
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Residues in contact with ILE 75 (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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73C MET* 4.0 25.8 - - + -
74C VAL* 1.3 77.6 - - - +
76C VAL* 1.3 68.3 + - - +
105C PHE* 3.4 38.4 - - + +
107C MET* 3.9 28.3 - - + -
117C ALA* 3.8 41.5 - - + +
120C LEU 5.8 0.2 - - - -
121C ALA* 5.2 1.1 - - - +
133C VAL* 4.4 6.7 - - + -
134C LEU 2.9 10.2 + - - +
135C VAL* 3.4 5.1 - - + +
136C ILE* 2.9 26.5 + - - +
120D LEU* 5.1 1.3 - - + -
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Residues in contact with VAL 76 (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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74C VAL* 4.8 2.9 - - + -
75C ILE* 1.3 77.9 - - - +
77C ALA* 1.3 65.2 + - - +
78C THR* 4.3 5.6 - - + -
88C ALA* 4.3 8.1 - - + -
89C ALA* 3.5 30.7 - - + +
92C ILE* 3.9 20.2 - - + -
105C PHE 3.0 7.9 + - - -
106C GLU* 3.1 25.9 - - + +
107C MET 2.9 23.7 + - - +
136C ILE* 3.2 11.9 - - + +
138C THR* 3.7 28.5 - - + -
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Residues in contact with ALA 77 (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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75C ILE 4.1 0.8 + - - -
76C VAL* 1.3 70.9 - - - +
78C THR* 1.3 63.4 + - - +
107C MET* 3.5 7.6 - - + +
113C ALA* 3.5 13.7 - - + +
114C ALA* 3.4 41.3 - - + +
117C ALA* 5.1 3.4 - - + -
135C VAL* 5.6 0.7 - - + -
136C ILE 2.8 10.4 + - - +
137C ALA* 4.3 0.9 - - - -
138C THR 3.0 25.6 + - - -
278C THR* 3.2 9.5 + - - -
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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