Contacts of the strand formed by residues 71 - 77 (chain C) in PDB entry 3GUT
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 THR 71 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C GLY* 1.3 81.9 - - - +
72C VAL* 1.3 59.0 + - - +
101C GLU* 5.3 9.4 + - - -
102C ALA 3.6 10.5 - - - -
103C ASP* 3.3 19.5 - - - +
104C LEU* 3.9 8.6 - - - +
162C GLN 4.2 0.4 - - - +
163C VAL* 3.6 0.5 - - - -
164C THR* 2.7 55.1 + - - +
166C ARG* 6.3 0.4 - - - +
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ILE* 4.5 4.3 - - + -
71C THR* 1.3 73.4 - - - +
73C ARG* 1.3 63.2 + - - +
74C ILE* 3.8 20.9 - - + -
100C TYR* 3.8 8.0 - - + +
101C GLU* 3.2 7.4 - - - +
102C ALA* 3.0 31.7 + - + +
103C ASP 4.7 2.0 - - - +
104C LEU* 3.4 29.6 - - + -
113C PHE* 3.8 28.5 - - + -
161C PHE* 5.0 0.2 - - + -
162C GLN 3.6 9.6 - - - +
163C VAL* 4.3 15.3 - - + -
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Residues in contact with ARG 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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72C VAL* 1.3 75.6 - - - +
74C ILE* 1.3 68.9 + - - +
99C TYR* 3.1 38.0 + - + -
100C TYR 3.1 11.0 - - - +
101C GLU* 3.0 35.6 + - + +
136C THR 5.0 3.0 + - - -
137C ASN 3.3 23.8 + - - -
138C ASN* 3.8 18.0 + - - +
160C CYS 3.3 3.8 - - - +
162C GLN* 3.0 64.4 + - + +
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Residues in contact with ILE 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 VAL* 3.8 15.5 - - + -
73C ARG* 1.3 79.2 - - - +
75C SER* 1.3 62.6 + - - +
90C LEU* 3.4 21.2 - - + +
99C TYR* 3.5 3.6 - - - -
100C TYR* 2.7 60.4 + - + -
113C PHE* 4.5 9.6 - - + -
116C LEU* 4.8 8.1 - - + -
159C LEU* 4.1 27.8 - - + -
160C CYS 3.8 2.2 - - - +
161C PHE* 2.8 46.0 - - + -
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Residues in contact with SER 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 ARG* 4.7 1.8 - - - -
74C ILE* 1.3 75.8 - - - +
76C LEU* 1.3 76.5 + - - +
77C VAL* 4.0 6.1 - - - +
85C PRO* 5.2 0.2 - - - +
99C TYR* 4.6 4.3 - - - -
138C ASN* 3.5 27.5 + - - -
140C PRO* 4.3 5.0 - - - +
158C ARG 3.5 2.3 - - - +
159C LEU* 3.5 1.2 - - - -
160C CYS* 2.7 44.7 + - - +
162C GLN* 3.0 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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74C ILE 4.3 0.4 + - - -
75C SER* 1.3 78.9 + - - +
77C VAL* 1.3 65.7 + - - +
85C PRO* 3.5 4.0 - - - +
86C HIS* 2.9 22.5 + - + +
88C HIS* 3.0 47.3 - - + +
89C GLU 3.9 2.2 - - - +
90C LEU* 3.1 46.2 - - + +
98C GLY 4.6 9.2 + - - +
118C ILE* 4.4 7.0 - - + -
138C ASN* 4.8 3.2 + - - +
157C VAL* 4.3 19.3 - - + -
158C ARG 3.7 11.4 - - - +
159C LEU* 4.0 10.8 - - + -
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Residues in contact with VAL 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 SER* 4.0 2.5 - - - +
76C LEU* 1.3 80.2 - - - +
78C THR* 1.3 71.3 + - - +
83C HIS* 4.1 18.4 - - + +
84C ARG 3.4 11.2 - - - +
85C PRO* 4.4 2.0 - - + -
86C HIS* 3.5 14.1 - - - +
140C PRO* 3.7 32.1 - - + -
157C VAL* 3.7 5.5 - - - -
158C ARG* 3.3 39.7 + - + +
160C CYS* 3.9 11.7 - - + -
179C LEU* 4.1 18.8 - - + -
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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