Contacts of the strand formed by residues 86 - 93 (chain C) in PDB entry 4TRZ
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 86 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C MET 3.8 0.2 - - - +
80C THR* 2.9 22.6 - - - -
81C VAL* 3.0 25.7 + - + +
84C PRO* 3.9 7.8 + - + +
85C PRO* 1.3 76.9 - - - +
87C THR* 1.3 63.7 + - - +
88C LEU* 3.9 6.2 + - + -
112C TYR 3.8 9.8 - - - +
113C TYR* 4.0 14.3 - - - -
114C GLN* 2.7 53.1 + - - +
117C LEU* 4.2 19.4 - - + +
118C SER* 4.8 4.2 - - - +
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Residues in contact with THR 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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78C GLU* 3.7 37.1 + - + +
79C MET 3.5 4.5 - - - +
80C THR* 4.2 10.2 - - + +
85C PRO* 5.2 1.6 + - - +
86C GLN* 1.3 73.6 - - - +
88C LEU* 1.3 70.5 + - - +
89C ASN* 4.7 4.7 - - - +
111C ARG* 3.4 31.6 + - - +
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Residues in contact with LEU 88 (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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77C VAL 3.7 0.3 - - - +
78C GLU* 3.5 2.4 - - - +
79C MET* 2.9 36.0 + - + +
81C VAL* 4.0 28.0 - - + -
86C GLN* 4.7 5.4 - - + +
87C THR* 1.3 84.4 - - - +
89C ASN* 1.3 67.2 + - - +
90C ILE* 3.7 15.7 + - + +
101C VAL* 4.1 28.5 - - + -
102C GLY 5.6 1.1 - - - +
111C ARG* 4.3 12.8 - - + +
112C TYR* 4.2 30.3 - - - +
113C TYR* 4.5 10.3 - - + +
177C GLU* 4.5 12.3 - - + +
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Residues in contact with ASN 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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76C TYR* 3.4 26.1 - - + -
77C VAL 3.5 5.2 - - - -
78C GLU* 4.4 17.6 - - - +
87C THR* 4.7 1.0 - - - +
88C LEU* 1.3 77.9 + - - +
90C ILE* 1.3 60.6 + - - +
111C ARG* 3.9 19.7 + - - +
175C ASN* 3.1 42.0 + - - +
176C TRP* 3.2 3.4 - - - -
177C GLU* 2.7 38.8 + - - +
178C GLY 3.4 2.8 + - - -
228C LEU* 4.5 5.3 - - - +
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Residues in contact with ILE 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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76C TYR* 3.1 3.8 - - - -
77C VAL* 2.8 34.2 + - + +
79C MET* 3.6 35.0 - - + -
88C LEU* 3.8 22.4 - - + +
89C ASN* 1.3 82.2 - - - +
91C LEU* 1.3 64.9 + - - +
92C VAL* 3.4 4.2 + - - +
99C PHE* 4.5 5.4 - - + -
101C VAL* 4.2 11.4 - - + -
178C GLY* 3.5 18.8 - - - -
179C ILE 3.4 8.1 - - - +
180C LEU* 3.2 41.7 - - + +
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Residues in contact with LEU 91 (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 GLY* 4.0 3.8 - - - -
75C TYR 3.4 15.7 - - - +
76C TYR* 3.8 3.9 - - - +
90C ILE* 1.3 73.1 - - - +
92C VAL* 1.3 75.3 + - - +
93C ASP* 3.6 17.4 + - + -
176C TRP* 3.5 45.3 - - + +
178C GLY 2.8 17.7 + - - +
179C ILE* 3.6 10.0 - - + -
180C LEU 2.6 33.1 + - - +
290C SER 5.9 0.2 - - - -
291C GLY* 4.8 2.5 - - - -
2F ILE* 3.5 33.2 - - + -
4F TVA 4.0 10.8 - - - -
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Residues in contact with VAL 92 (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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67C LEU* 4.5 12.1 - - + -
75C TYR* 3.0 20.7 + - + +
76C TYR* 4.2 4.7 - - - -
77C VAL* 4.0 19.5 - - + +
90C ILE 3.8 9.9 - - - +
91C LEU* 1.3 79.8 - - - +
93C ASP* 1.3 54.3 + - - +
94C THR* 5.3 0.2 - - + -
180C LEU* 3.8 8.3 - - + +
182C LEU* 3.7 31.2 - - + -
213C LEU* 4.4 11.9 - - + -
235C MET* 4.0 17.0 - - + -
290C SER* 2.3 28.5 + - - +
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Residues in contact with ASP 93 (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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91C LEU* 3.6 15.9 + - + -
92C VAL* 1.3 74.5 - - - +
94C THR* 1.3 61.7 + - - +
95C GLY 2.4 31.2 + - - -
96C SER* 3.4 15.1 + - - +
179C ILE* 4.1 5.3 - - + +
180C LEU 2.7 17.3 + - - +
181C GLY* 3.0 3.5 - - - -
182C LEU* 2.8 24.9 + - - -
289C ASP* 2.6 17.5 - - - +
290C SER* 2.9 2.7 - - - -
291C GLY* 3.8 7.9 - - - -
4F TVA 2.3 39.7 + - - +
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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