Contacts of the helix formed by residues 173 - 180 (chain A) in PDB entry 3C2B
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 ASP 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A SER* 1.3 81.9 + - - +
174A LEU* 1.3 64.7 + - - +
175A HIS 3.2 3.0 + - - -
176A VAL* 3.4 13.8 + - + +
177A ARG* 3.0 47.5 + - + +
134B ARG* 3.4 24.9 + - - +
164B ARG* 5.3 1.9 + - - +
167B TYR* 3.6 25.1 - - + +
301B FMT 3.7 19.2 - - - +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.8 27.4 - - + -
171A VAL* 2.7 25.4 + - + +
172A SER 3.3 0.2 - - - -
173A ASP* 1.3 77.0 + - - +
175A HIS* 1.3 60.2 + - - +
177A ARG* 3.5 9.5 + - + +
178A MSE 3.0 48.6 + - + +
182A GLU* 4.8 12.3 - - - +
184A PRO* 4.7 11.4 - - + -
185A ASP 5.4 2.0 - - - +
188A PHE* 4.0 19.7 - - + -
191A ARG* 6.3 0.7 - - + -
164B ARG* 4.6 8.3 - - - +
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Residues in contact with HIS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.7 47.5 + - + +
107A SER* 5.0 1.2 + - - -
108A LEU* 4.0 11.1 - - + +
111A ASN* 4.4 19.6 + - - -
167A TYR* 4.7 6.1 + - + +
171A VAL* 3.8 20.8 - - + +
172A SER 5.7 0.2 - - - +
173A ASP 3.2 1.2 + - - -
174A LEU* 1.3 76.5 - - - +
176A VAL* 1.3 58.1 + - - +
178A MSE 3.2 8.6 + - + +
179A LEU* 2.9 54.0 + - + +
176B VAL* 3.6 33.9 - - + +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 3.4 15.5 + - + +
175A HIS* 1.3 74.9 - - - +
177A ARG* 1.3 64.7 + - + +
179A LEU* 3.1 9.7 + - + +
180A LEU* 3.0 38.4 + - + +
111B ASN* 4.4 5.6 - - - +
115B ILE* 4.6 2.7 - - + -
175B HIS* 3.6 41.7 - - + +
176B VAL* 3.7 23.8 - - + +
179B LEU* 4.0 13.5 - - + -
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 3.0 47.4 + - + +
174A LEU* 3.8 12.8 - - + +
175A HIS 3.4 0.2 - - - -
176A VAL* 1.3 76.0 - - + +
178A MSE 1.3 58.9 + - - +
180A LEU* 3.3 6.9 + - + +
181A GLY 3.2 5.5 + - - -
182A GLU* 2.6 65.4 + - + +
129B LEU 5.4 0.6 + - - -
130B LEU* 3.6 52.3 + - + +
134B ARG* 5.2 7.9 - - - +
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Residues in contact with MSE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 4.6 2.0 - - + +
102A LEU* 3.7 18.6 - - + +
103A ALA* 3.6 47.3 - - + +
108A LEU* 3.8 15.1 - - + +
112A ARG* 2.8 17.3 + - - -
174A LEU* 3.0 47.5 + - + +
175A HIS* 3.7 9.6 - - + +
177A ARG* 1.3 72.1 - - - +
179A LEU* 1.3 58.0 + - - +
181A GLY* 2.8 20.8 + - - -
182A GLU* 3.2 21.3 + - + +
184A PRO* 3.7 24.2 - - + -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 3.6 38.6 - - + +
111A ASN* 3.8 15.0 - - + -
112A ARG* 2.9 31.8 + - + +
115A ILE* 3.7 25.6 - - + -
175A HIS* 2.9 43.4 + - + +
176A VAL* 3.1 11.0 + - + +
178A MSE 1.3 77.4 - - - +
180A LEU* 1.3 58.3 + - - +
115B ILE* 4.0 18.8 - - + +
118B ALA* 3.7 8.1 - - - +
176B VAL* 4.3 7.9 - - + -
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 3.0 32.3 + - + +
177A ARG* 3.5 8.3 - - + +
178A MSE 3.2 0.2 - - - -
179A LEU* 1.3 76.0 - - - +
181A GLY* 1.3 58.8 + - - +
182A GLU 3.6 0.7 - - - -
111B ASN* 4.0 10.8 - - - +
114B ALA* 3.6 25.8 - - + -
115B ILE* 3.6 24.0 - - + +
118B ALA* 4.5 3.4 - - - +
122B GLY* 3.6 12.8 - - - -
123B SER 4.1 0.5 + - - -
126B GLY* 3.9 21.0 - - - +
127B ASP* 5.4 0.9 - - - +
129B LEU* 3.8 23.6 - - + -
130B LEU* 3.8 31.8 - - + +
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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