Contacts of the helix formed by residues 93 - 103 (chain C) in PDB entry 3Q2S
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 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B ALA 3.8 12.1 - - - +
164B HIS 3.3 15.0 - - - -
166B THR* 3.2 23.4 - - + +
91C TRP 3.1 17.7 - - - +
92C THR* 1.3 73.0 - - - +
94C ASP* 1.3 66.3 - - - +
95C GLU* 2.7 12.5 + - - +
96C ASP* 2.5 44.7 + - - +
97C LEU* 2.8 6.3 + - - -
114C PHE* 4.0 2.2 - - - -
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Residues in contact with ASP 94 (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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164B HIS 2.8 24.8 - - - +
165B ILE* 3.9 14.6 - - - +
166B THR* 2.7 25.1 + - - -
167B LYS* 4.6 3.2 + - - +
93C THR* 1.3 67.9 - - - +
95C GLU* 1.3 66.9 + - - +
97C LEU* 3.5 5.3 + - - +
98C THR* 2.9 29.0 + - - -
112C ILE* 3.7 30.8 - - + +
114C PHE* 3.4 25.8 - - + -
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR* 3.0 29.0 + - + +
167B LYS* 4.3 22.1 - - - +
93C THR* 2.7 13.2 + - - +
94C ASP* 1.3 84.3 + - - +
96C ASP* 1.3 57.3 + - + +
98C THR* 2.9 24.0 + - - -
99C GLU* 3.0 21.5 + - + +
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Residues in contact with ASP 96 (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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92C THR* 3.3 12.1 - - - +
93C THR* 2.5 49.1 + - - +
95C GLU* 1.3 72.0 - - - +
97C LEU* 1.3 86.5 + - - +
98C THR 3.0 1.6 - - - -
99C GLU* 3.0 34.7 + - - +
100C ALA* 3.2 11.8 + - - +
149C LEU* 4.7 6.2 - - + +
150C HIS* 3.4 22.1 + - + -
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Residues in contact with LEU 97 (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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85C ILE* 4.6 25.6 - - + -
88C LEU* 3.9 26.2 - - + -
92C THR* 4.4 3.6 - - + -
93C THR 2.8 12.5 + - - +
94C ASP 3.6 5.8 - - - +
96C ASP* 1.3 85.9 + - - +
98C THR* 1.3 60.4 + - - +
100C ALA* 3.6 3.6 + - + +
101C VAL* 3.5 23.2 + - + +
112C ILE* 4.2 17.7 - - + -
114C PHE* 4.1 15.5 - - + -
127C ALA* 4.4 7.4 - - + -
129C VAL* 6.2 1.6 - - + -
144C LEU* 5.3 4.3 - - + -
149C LEU* 3.3 31.2 - - + -
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Residues in contact with THR 98 (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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94C ASP 2.9 17.1 + - - -
95C GLU* 2.9 15.9 + - - -
97C LEU* 1.3 76.2 - - - +
99C GLU* 1.3 64.7 + - - +
101C VAL* 3.1 7.3 + - - +
102C HIS* 3.0 57.8 + - + +
109C ILE* 4.6 19.9 - - + +
112C ILE* 4.9 7.1 - - - +
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Residues in contact with GLU 99 (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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95C GLU* 3.0 18.4 + - + +
96C ASP* 3.0 26.7 + - - +
98C THR* 1.3 79.0 - - + +
100C ALA* 1.3 64.8 + - - +
102C HIS* 3.8 6.3 + - - +
103C SER* 3.2 24.6 + - - -
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Residues in contact with ALA 100 (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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96C ASP 3.2 3.0 + - - +
97C LEU* 3.7 10.5 - - + +
98C THR 3.2 0.6 - - - -
99C GLU* 1.3 82.2 - - - +
101C VAL* 1.3 65.0 + - + +
103C SER* 3.3 17.7 + - - +
104C LEU* 3.7 9.2 - - - +
144C LEU* 4.6 16.2 - - + -
147C ARG* 6.1 2.7 - - + -
149C LEU* 3.5 34.5 - - + -
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Residues in contact with VAL 101 (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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85C ILE* 5.4 12.1 - - + -
97C LEU* 3.5 17.9 + - + +
98C THR* 3.1 10.6 + - - +
100C ALA* 1.3 72.6 - - + +
102C HIS* 1.3 70.5 + - - +
103C SER 2.7 3.1 + - - -
104C LEU* 2.7 28.4 + - + +
105C GLY 3.9 0.3 + - - -
106C VAL* 3.6 35.9 + - + +
109C ILE* 4.0 18.2 - - + -
140C LEU* 4.5 17.7 - - + -
144C LEU* 5.5 6.5 - - + -
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Residues in contact with HIS 102 (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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98C THR* 3.0 36.0 + - + +
99C GLU* 4.1 6.5 - - - +
101C VAL* 1.3 75.3 - - - +
103C SER* 1.3 55.1 + - - +
104C LEU 2.8 12.0 + - - -
105C GLY* 2.9 13.9 + - - -
106C VAL 3.2 9.8 + - - -
107C ASN* 3.6 25.7 + - + +
109C ILE* 3.0 35.0 - - + +
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Residues in contact with SER 103 (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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99C GLU 3.2 16.9 + - - -
100C ALA* 3.3 9.0 + - - +
101C VAL 2.7 5.6 + - - -
102C HIS* 1.3 72.9 - - - +
104C LEU* 1.3 66.1 + - - +
105C GLY 3.7 0.2 - - - -
147C ARG* 5.7 0.5 + - - -
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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