Contacts of the strand formed by residues 71 - 77 (chain C) in PDB entry 3S52
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C GLU* 1.3 71.7 - - - +
72C GLU* 1.3 65.1 + - - +
98C VAL* 3.6 27.6 - - + -
99C ALA 3.4 7.4 - - - +
100C LEU* 4.0 13.4 - - + +
147C LEU* 4.2 11.7 - - + -
148C SER 3.4 36.8 - - - +
149C LEU* 4.1 8.7 - - + +
157C GLN* 3.0 37.6 + - + +
191C THR* 2.7 22.6 + - - -
192C PRO* 3.4 12.8 - - + +
206C ILE* 3.8 10.1 - - + -
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Residues in contact with GLU 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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21C CYS* 5.2 2.0 - - - +
22C VAL 4.6 5.1 - - - +
44C PHE* 5.5 0.2 - - - -
70C GLU* 3.4 13.1 - - - +
71C ILE* 1.3 83.7 - - - +
73C LEU* 1.3 66.3 + - - +
74C ALA 3.5 0.2 + - - -
98C VAL* 3.5 5.4 - - - +
99C ALA* 2.9 32.7 + - - +
101C ASP* 3.2 34.6 - - + +
147C LEU* 4.1 8.5 - - - -
188C LEU* 3.3 24.6 - - + +
189C THR 4.5 0.4 - - - +
190C GLY* 2.9 41.7 + - - +
191C THR* 3.7 13.5 + - - +
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLU* 1.3 72.8 - - - +
74C ALA* 1.3 66.2 + - - +
75C VAL* 4.4 3.8 - - + -
96C TYR* 4.1 12.3 - - + -
97C GLY 3.5 15.9 - - - +
139C PHE* 3.7 30.1 - - + -
142C ALA* 3.9 11.7 - - + +
145C ALA* 4.5 4.3 - - + -
147C LEU* 3.8 12.1 - - + +
161C THR* 3.9 18.8 - - + -
168C ILE* 3.6 31.2 - - + -
188C LEU* 3.8 1.4 - - - -
189C THR* 2.8 48.8 + - - +
190C GLY 4.3 0.6 + - - -
208C LEU* 4.1 9.6 - - + -
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Residues in contact with ALA 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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72C GLU 3.5 1.2 + - - -
73C LEU* 1.3 75.0 - - - +
75C VAL* 1.3 63.3 + - - +
76C LEU 4.3 0.2 - - - -
96C TYR* 3.4 6.4 - - - +
97C GLY 2.8 40.7 + - - +
98C VAL 4.3 1.3 - - - +
99C ALA* 4.4 2.9 - - + -
130C ILE* 3.6 25.8 - - + -
133C PHE* 4.3 4.5 - - + -
186C ILE* 4.1 2.9 - - + -
187C VAL 3.4 4.5 - - - -
188C LEU* 3.6 21.1 - - + -
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 4.4 3.4 - - + -
74C ALA* 1.3 77.6 - - - +
76C LEU* 1.3 65.3 + - - +
77C ILE* 3.7 4.3 + - + +
93C ILE* 3.8 31.0 - - + -
95C GLY 3.7 3.8 - - - +
96C TYR* 3.9 18.4 - - + -
133C PHE* 4.4 2.7 - - - -
168C ILE* 4.2 9.4 - - + -
172C ILE* 4.0 19.5 - - + -
186C ILE* 3.4 4.6 - - - -
187C VAL* 2.8 44.6 + - + +
189C THR* 3.8 25.6 - - + -
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Residues in contact with LEU 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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39A VAL* 4.8 2.9 - - + -
4C HIS* 4.2 17.5 - - + +
12C LEU* 3.8 28.7 - - + -
14C PHE* 4.0 17.9 - - + -
75C VAL* 1.3 72.2 - - - +
77C ILE* 1.3 69.6 + - - +
93C ILE* 3.8 4.0 - - - -
94C ALA* 2.9 34.3 + - + -
95C GLY 2.9 20.0 + - - +
133C PHE* 3.7 30.0 - - + -
184C GLY* 4.1 17.9 - - - +
185C ASP 3.8 9.6 - - - +
186C ILE* 4.4 3.8 - - + +
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Residues in contact with ILE 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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14C PHE* 4.6 0.5 - - - -
75C VAL* 4.3 6.1 - - + +
76C LEU* 1.3 78.5 - - - +
78C GLY* 1.3 57.0 + - - +
79C THR 3.1 26.5 - - - +
81C LEU* 4.1 24.5 - - + -
92C ALA 4.1 3.8 - - - +
93C ILE* 4.8 7.0 - - + -
172C ILE* 4.2 18.2 - - + -
181C LEU* 4.2 14.8 - - + +
182C ARG 3.8 13.9 - - - +
183C ALA* 3.4 0.3 - - - -
184C GLY* 2.7 32.9 + - - -
185C ASP* 2.9 20.8 + - + +
187C VAL* 4.0 26.9 - - + -
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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