Contacts of the helix formed by residues 135 - 142 (chain C) in PDB entry 3C5C
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 LYS 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C GLY 2.8 30.1 + - - -
31C ALA 3.6 10.5 - - - -
99C SER* 3.6 20.8 + - - -
100C VAL* 3.3 12.6 - - + +
101C ASP* 4.0 15.6 + - - +
134C ASN* 1.3 92.4 + - - +
136C LEU* 1.3 60.6 + - - +
137C ASP* 3.1 14.4 - - - +
138C MET* 2.8 29.3 + - + +
163C VAL 3.1 0.6 + - - -
201C GDP 2.9 58.8 + - + +
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Residues in contact with LEU 136 (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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100C VAL* 4.3 6.5 - - + -
133C GLY 5.1 0.2 - - - -
134C ASN 3.3 1.2 - - - -
135C LYS* 1.3 76.7 - - - +
137C ASP* 1.3 62.1 + - - +
138C MET 3.0 0.2 - - - -
139C ALA* 3.0 28.2 + - + +
142C ARG* 3.5 15.9 - - - +
162C GLU* 3.2 49.6 - - + +
163C VAL* 2.9 22.6 + - - +
164C SER* 3.9 3.1 - - - -
167C LEU* 4.7 11.2 - - + -
171C HIS* 5.7 3.1 - - + +
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Residues in contact with ASP 137 (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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135C LYS* 3.3 6.4 - - - -
136C LEU* 1.3 72.3 - - - +
138C MET* 1.3 64.6 + - - +
139C ALA* 3.3 2.8 + - - -
140C GLN* 5.1 0.9 + - - +
164C SER* 2.8 25.8 + - - +
166C CYS* 3.4 14.3 - - - -
167C LEU* 3.8 24.1 - - + +
201C GDP 2.7 41.8 + - - -
89D ASN* 4.6 4.3 - - + +
90D TRP* 5.9 1.0 - - - -
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Residues in contact with MET 138 (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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100C VAL* 4.7 1.5 - - - +
101C ASP* 4.0 28.3 - - + +
135C LYS* 2.8 21.1 + - + +
137C ASP* 1.3 85.9 - - - +
139C ALA* 1.3 56.9 - - - +
140C GLN* 3.1 3.8 - - - -
141C TYR* 2.9 29.1 + - + -
142C ARG* 3.4 7.4 + - - -
201C GDP 2.9 28.3 - - + +
22D ASN* 5.2 4.0 - - - +
89D ASN 3.2 19.3 - - - +
90D TRP* 3.7 39.7 - - + +
125D ARG* 5.7 0.7 - - - +
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Residues in contact with ALA 139 (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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100C VAL* 4.8 2.5 - - - -
136C LEU* 3.0 21.6 + - + +
137C ASP 3.3 3.0 + - - -
138C MET* 1.3 75.4 - - - +
140C GLN* 1.3 61.1 + - - +
141C TYR 3.1 0.2 - - - -
142C ARG* 3.2 50.1 + - - +
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Residues in contact with GLN 140 (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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137C ASP 5.1 0.8 + - - +
138C MET* 3.1 2.1 + - - +
139C ALA* 1.3 76.5 - - - +
141C TYR* 1.3 57.2 + - + +
142C ARG 3.5 0.6 + - - -
90D TRP* 6.4 0.4 - - - +
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Residues in contact with TYR 141 (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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101C ASP* 3.6 19.4 - - + +
138C MET* 2.9 18.2 + - + +
140C GLN* 1.3 79.3 - - + +
142C ARG* 1.3 65.3 + - - +
143C GLN* 3.4 7.4 + - - +
20D GLU* 5.4 11.4 - - - +
90D TRP* 5.9 4.7 - - - +
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Residues in contact with ARG 142 (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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100C VAL* 3.4 19.4 - - + +
101C ASP* 4.3 0.2 - - - +
136C LEU* 3.5 16.4 - - - +
138C MET 3.4 2.9 + - - -
139C ALA* 3.2 37.0 + - - +
140C GLN 3.5 1.0 - - - -
141C TYR* 1.3 79.3 - - - +
143C GLN* 1.3 60.4 + - - +
144C VAL 2.8 30.9 + - - +
145C THR* 4.4 8.5 - - + +
146C LYS* 3.6 13.8 - - - +
162C GLU* 2.8 41.2 + - - -
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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