Contacts of the helix formed by residues 137 - 146 (chain C) in PDB entry 3C3P
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 ASN 137 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU* 5.4 0.5 - - - +
136C PHE* 1.3 69.6 - - - +
138C GLY* 1.3 65.6 + - - +
139C ALA* 3.5 14.5 + - - +
140C ASP* 3.0 32.5 + - + +
141C VAL* 3.1 13.5 + - - +
179C ARG* 5.1 11.0 + - - +
180C GLU* 5.8 2.4 - - - +
181C PHE* 5.6 2.3 + - - +
221C EDO 3.6 15.0 + - - +
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Residues in contact with GLY 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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131C MSE 4.0 14.4 - - - -
133C CYS* 6.1 0.8 - - - -
136C PHE 3.4 6.8 + - - -
137C ASN* 1.3 74.2 + - - +
139C ALA* 1.3 55.8 + - - +
141C VAL* 3.1 3.6 + - - +
142C LEU* 2.9 26.3 + - - +
181C PHE* 3.2 45.4 - - - +
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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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19B GLU* 3.8 22.7 - - - +
137C ASN* 3.3 13.0 + - - +
138C GLY* 1.3 73.9 - - - +
140C ASP* 1.3 58.7 + - - +
142C LEU* 3.3 2.5 + - - +
143C GLU* 2.9 28.6 + - - +
181C PHE* 3.2 13.3 - - - +
184C HIS* 3.9 25.2 + - + +
188C ARG* 5.5 0.3 + - - -
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Residues in contact with ASP 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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117C LEU* 5.9 2.2 - - + -
137C ASN* 3.0 30.3 + - + +
139C ALA* 1.3 78.2 - - - +
141C VAL* 1.3 64.7 + - + +
143C GLU* 3.3 7.3 + - - +
144C ARG* 3.2 30.2 + - + +
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Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO* 6.0 1.1 - - + -
117C LEU* 3.8 31.4 - - + -
129C LEU* 4.2 15.7 - - + -
131C MSE 4.3 23.1 - - + -
136C PHE* 3.6 27.4 - - + -
137C ASN 3.1 15.4 + - - +
138C GLY 3.1 7.4 + - - +
140C ASP* 1.3 77.8 - - + +
142C LEU* 1.3 52.6 + - - +
144C ARG* 3.3 3.0 + - - -
145C MSE 2.7 57.0 + - + +
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Residues in contact with LEU 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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129C LEU* 5.7 1.3 - - + -
131C MSE 5.6 0.7 - - + -
138C GLY 2.9 15.8 + - - +
139C ALA* 3.9 4.0 - - - +
141C VAL* 1.3 76.2 - - + +
143C GLU* 1.3 66.0 + - - +
145C MSE 4.3 2.9 - - + +
146C ASN* 2.9 35.6 + - + +
149C LEU* 4.2 16.4 - - + -
155C LEU* 4.5 15.5 - - + -
181C PHE* 4.2 12.8 - - + -
184C HIS* 4.4 0.9 - - - +
185C LEU* 3.5 31.0 - - + -
188C ARG* 3.2 35.6 + - - +
191C PHE* 3.9 23.1 - - + -
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Residues in contact with GLU 143 (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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139C ALA 2.9 17.6 + - - +
140C ASP* 3.5 10.3 - - - +
141C VAL 3.2 0.4 - - - -
142C LEU* 1.3 78.5 - - - +
144C ARG* 1.3 66.6 + - + +
146C ASN* 4.6 3.3 + - - +
147C ARG* 5.4 2.1 + - - +
188C ARG* 5.3 3.1 - - - +
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Residues in contact with ARG 144 (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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117C LEU* 3.0 50.5 + - - +
118C GLY* 4.9 2.8 - - - -
121C ALA* 4.8 14.3 - - + +
140C ASP* 3.2 18.6 + - + +
141C VAL* 3.8 3.8 - - - +
143C GLU* 1.3 84.7 - - + +
145C MSE 1.3 65.4 + - + +
146C ASN 3.7 0.2 - - - -
147C ARG* 3.5 19.9 - - - +
148C CYS* 4.3 3.6 - - - -
213C EDO 3.2 34.5 + - - -
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Residues in contact with MSE 145 (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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117C LEU* 4.6 11.4 - - + +
120C ALA* 3.6 25.4 - - + +
121C ALA* 3.8 30.5 - - - -
126C ILE* 3.2 35.7 - - + -
129C LEU* 4.0 24.5 - - + -
141C VAL* 2.7 39.6 + - + +
142C LEU* 4.7 2.0 - - + -
144C ARG* 1.3 78.5 - - + +
146C ASN* 1.3 55.2 + - - +
147C ARG 3.0 3.6 - - - -
148C CYS* 2.6 39.6 + - + +
149C LEU* 3.3 7.7 + - + +
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Residues in contact with ASN 146 (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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142C LEU* 2.9 25.0 + - + +
143C GLU 4.6 2.4 + - - +
144C ARG 3.7 0.4 - - - -
145C MSE 1.3 76.7 - - - +
147C ARG* 1.3 56.8 - - - +
149C LEU* 3.0 34.1 + - - +
188C ARG* 3.8 22.8 - - - +
190C ASP* 4.1 7.5 + - - -
191C PHE* 3.9 6.0 - - - -
207C ARG* 3.2 40.9 + - - +
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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