Contacts of the helix formed by residues 158 - 172 (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 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A PHE* 3.4 8.5 - - - +
157A ASP* 1.3 86.0 - - + +
159A ALA* 1.3 67.4 + - - +
160A GLU* 3.0 23.5 + - - +
161A GLU* 3.3 24.9 + - + +
162A ALA* 3.2 17.2 + - - +
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Residues in contact with ALA 159 (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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142A ARG* 6.2 0.6 - - - +
145A ILE* 4.5 8.1 - - + +
146A GLU* 5.7 3.1 - - - +
156A PHE* 3.4 33.7 - - + -
158A ASP* 1.3 75.1 + - - +
160A GLU* 1.3 58.6 + - + +
162A ALA* 3.4 4.3 + - - +
163A TYR* 3.1 24.8 + - - +
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Residues in contact with GLU 160 (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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142A ARG* 4.5 23.1 + - - +
158A ASP* 3.0 15.4 + - - +
159A ALA* 1.3 76.8 - - + +
161A GLU* 1.3 55.7 + - - +
163A TYR* 3.3 8.1 + - - +
164A ARG* 2.8 33.1 + - - +
302A FMT 4.2 3.1 - - - +
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Residues in contact with GLU 161 (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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158A ASP* 3.3 27.1 + - + +
160A GLU* 1.3 75.7 - - - +
162A ALA* 1.3 61.8 + - - +
164A ARG* 3.5 10.9 + - - +
165A SER* 2.9 38.6 + - - -
203A TYR* 4.1 8.7 - - + +
191B ARG* 2.6 46.9 + - - -
194B LYS* 4.0 19.0 + - - +
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Residues in contact with ALA 162 (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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145A ILE* 4.3 2.9 - - + -
156A PHE* 3.9 30.1 - - + -
158A ASP 3.2 10.4 + - - +
159A ALA 3.5 9.6 - - - +
161A GLU* 1.3 77.2 - - - +
163A TYR* 1.3 61.3 + - - +
165A SER* 3.4 1.6 + - - -
166A PHE 3.1 17.8 + - - -
199A PHE* 3.3 24.9 - - + -
203A TYR* 3.7 22.1 + - + -
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Residues in contact with TYR 163 (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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94A PHE* 4.0 11.7 - + - -
137A ILE* 3.5 18.5 - - - +
138A ASP* 2.7 44.5 + - + -
141A ALA* 3.4 28.7 - - + -
142A ARG* 4.2 25.1 - - + -
145A ILE* 3.7 19.2 - - + +
159A ALA 3.1 11.9 + - - +
160A GLU* 3.3 8.3 + - - +
161A GLU 3.3 0.2 - - - -
162A ALA* 1.3 74.3 - - - +
164A ARG* 1.3 55.1 + - - +
166A PHE* 3.2 7.7 + + + -
167A TYR* 2.8 60.2 + + + +
302A FMT 3.7 18.4 - - - -
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Residues in contact with ARG 164 (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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160A GLU 2.8 21.6 + - - +
161A GLU* 3.3 14.1 + - - +
163A TYR* 1.3 74.0 - - - +
165A SER* 1.3 58.1 + - - +
167A TYR* 3.4 0.3 + - - +
168A GLY* 3.0 14.9 + - - -
302A FMT 3.4 17.4 + - - +
168B GLY 4.9 0.3 - - - +
169B LEU 3.0 24.7 + - - -
170B ILE 2.7 22.0 + - - -
171B VAL* 3.4 16.0 + - - +
172B SER* 2.6 42.6 + - - +
173B ASP* 5.3 2.3 + - - +
174B LEU* 4.7 6.3 - - - +
185B ASP* 4.7 12.9 + - - -
191B ARG* 3.2 48.8 - - - +
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Residues in contact with SER 165 (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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161A GLU* 2.9 21.6 + - - -
162A ALA 3.6 2.9 - - - -
164A ARG* 1.3 72.0 + - - +
166A PHE* 1.3 61.9 + - - +
168A GLY* 3.2 2.4 + - - -
169A LEU* 2.9 35.6 + - - +
202A LEU* 4.5 5.4 - - - +
203A TYR* 2.8 35.3 + - - -
169B LEU* 4.1 26.3 - - - +
198B ALA* 5.3 3.1 - - - +
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Residues in contact with PHE 166 (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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91A LEU* 3.7 45.5 - - + -
94A PHE* 3.6 28.3 - + - -
95A ALA* 4.4 0.7 - - + -
141A ALA* 5.5 1.3 - - + -
145A ILE* 4.8 6.5 - - + -
162A ALA 3.1 12.4 + - - +
163A TYR* 3.5 16.6 - + - +
165A SER* 1.3 77.5 - - - +
167A TYR* 1.3 58.7 + - - +
169A LEU* 3.3 4.8 + - + +
170A ILE* 2.9 56.4 + - + +
195A ALA 3.9 16.2 - - - -
196A VAL* 4.0 14.1 - - + -
199A PHE* 3.6 36.5 - + + -
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Residues in contact with TYR 167 (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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98A LEU* 3.7 20.6 - - + -
102A LEU* 3.9 18.4 - - - +
134A ARG* 3.5 48.7 + - - -
163A TYR* 2.8 41.7 + + + +
164A ARG 3.6 4.7 - - - +
166A PHE* 1.3 78.5 - - - +
168A GLY* 1.3 63.8 + - - +
170A ILE* 3.3 8.0 + - - +
171A VAL* 3.0 47.9 + - + +
175A HIS* 4.7 6.3 + - + -
302A FMT 4.3 6.1 - - - -
172B SER* 3.9 7.4 - - - +
173B ASP* 3.5 28.0 - - + +
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Residues in contact with GLY 168 (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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164A ARG 3.0 11.7 + - - -
165A SER 3.8 1.8 - - - -
167A TYR* 1.3 76.9 - - - +
169A LEU* 1.3 58.3 + - - +
172A SER* 2.7 35.4 + - - -
168B GLY* 3.3 33.2 - - - -
172B SER* 3.6 14.1 + - - -
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Residues in contact with LEU 169 (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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165A SER* 2.9 24.1 + - - +
166A PHE* 3.6 6.1 - - - +
168A GLY* 1.3 74.3 - - - +
170A ILE* 1.3 60.3 + - - +
191A ARG* 4.2 2.1 + - - -
195A ALA* 3.8 20.1 - - + +
198A ALA* 3.8 22.9 - - + -
199A PHE* 3.9 16.8 - - - +
202A LEU* 3.9 20.2 - - + -
164B ARG* 2.9 23.1 + - - +
165B SER* 4.1 21.7 - - - +
168B GLY* 4.5 0.8 - - - -
169B LEU* 3.9 19.3 - - + -
202B LEU* 3.9 22.7 - - + -
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Residues in contact with ILE 170 (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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94A PHE* 4.0 10.5 - - + -
95A ALA* 3.6 36.3 - - + +
98A LEU* 4.1 9.4 - - + -
99A LEU* 3.6 32.8 - - + +
166A PHE* 2.9 52.8 + - + +
167A TYR* 3.8 3.4 - - - +
169A LEU* 1.3 73.0 - - - +
171A VAL* 1.3 61.9 + - + +
191A ARG* 3.4 10.9 - - + +
195A ALA* 3.6 22.4 - - + -
164B ARG* 2.8 23.2 + - - -
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Residues in contact with VAL 171 (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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98A LEU* 3.8 20.6 - - + -
99A LEU* 4.3 8.7 - - + -
102A LEU* 3.5 26.7 - - + -
167A TYR* 3.0 30.0 + - + +
168A GLY* 5.2 0.2 - - - -
170A ILE* 1.3 81.9 - - + +
172A SER* 1.3 80.4 + - - +
173A ASP 3.1 0.2 + - - -
174A LEU* 2.7 26.5 + - + +
175A HIS* 3.8 32.3 - - + +
164B ARG* 3.5 3.0 + - - +
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Residues in contact with SER 172 (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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168A GLY* 2.7 26.7 + - - -
170A ILE 3.7 0.4 - - - -
171A VAL* 1.3 82.3 - - - +
173A ASP* 1.3 72.6 + - - -
174A LEU 3.4 0.5 + - - -
175A HIS* 4.7 0.3 + - - +
164B ARG* 3.0 54.4 + - - +
167B TYR* 3.9 13.5 - - - +
168B GLY* 3.8 11.8 + - - -
172B SER 4.4 12.9 - - - +
301B FMT 3.9 1.0 - - - -
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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