Contacts of the helix formed by residues 159 - 172 (chain C) in PDB entry 4B94
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 VAL 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C LEU* 4.0 18.6 - - + +
157C GLY* 3.3 17.0 + - - +
158C ASN* 1.3 68.3 - - - +
160C LYS* 1.3 64.5 + - - +
162C SER* 3.4 8.2 + - - -
163C LYS* 3.1 23.4 + - + +
187C LEU* 4.2 21.6 - - + +
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Residues in contact with LYS 160 (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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158C ASN 3.4 0.2 - - - -
159C VAL* 1.3 77.9 - - - +
161C LYS* 1.4 57.6 + - - +
163C LYS* 3.4 7.2 + - - +
164C GLN* 3.0 56.8 + - + +
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Residues in contact with LYS 161 (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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130A ASP* 3.5 30.1 + - - -
133A GLN* 5.2 2.0 + - - -
129C ARG* 6.0 2.0 - - - +
133C GLN* 5.4 1.7 - - - +
136C ARG* 5.0 0.6 - - - +
149C PHE* 5.0 7.2 - - - -
153C GLU* 3.8 26.7 - - + +
158C ASN* 3.5 19.5 + - + +
159C VAL 3.4 0.2 - - - -
160C LYS* 1.4 74.7 - - - +
162C SER* 1.4 58.9 + - - +
164C GLN* 3.3 21.4 + - + +
165C LEU* 2.9 52.0 + - + +
168C LYS* 5.4 1.2 - - - +
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Residues in contact with SER 162 (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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150C ALA* 2.7 39.9 + - - +
153C GLU* 4.0 4.7 - - - +
154C LEU* 3.8 16.6 - - - +
158C ASN 3.0 17.7 + - - -
159C VAL* 3.5 9.0 - - - -
160C LYS 3.3 0.2 - - - -
161C LYS* 1.4 76.5 - - - +
163C LYS* 1.4 61.0 + - - +
165C LEU 3.5 0.5 + - - -
166C LEU* 3.2 25.1 + - - +
187C LEU* 3.8 16.0 - - - +
194C LEU* 4.1 2.9 - - - +
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Residues in contact with LYS 163 (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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159C VAL* 3.1 13.6 + - + +
160C LYS* 3.7 10.5 - - - +
161C LYS 3.3 0.2 - - - -
162C SER* 1.4 73.5 - - - +
164C GLN* 1.4 58.7 + - + +
166C LEU* 3.3 4.7 + - - +
167C GLN* 2.9 63.2 + - - +
184C LEU* 4.3 12.3 - - + -
187C LEU* 3.5 20.3 - - + +
188C ASN* 4.4 15.5 + - - -
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Residues in contact with GLN 164 (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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160C LYS* 3.0 51.4 + - + +
161C LYS* 3.6 26.0 + - + +
163C LYS* 1.4 74.2 - - + +
165C LEU* 1.3 56.3 + - - +
167C GLN* 3.8 13.1 - - - +
168C LYS* 2.9 32.9 + - - +
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Residues in contact with LEU 165 (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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136C ARG* 3.5 36.0 + - - +
146C HIS* 4.5 12.3 + - + +
149C PHE* 3.7 32.3 - - + -
150C ALA* 3.9 17.9 - - + +
153C GLU* 3.7 31.0 - - + -
161C LYS* 2.9 37.6 + - + +
162C SER 3.7 5.2 - - - +
163C LYS 3.3 0.2 - - - -
164C GLN* 1.3 74.1 - - - +
166C LEU* 1.3 61.0 + - - +
168C LYS* 3.5 5.0 + - - +
169C ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 166 (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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146C HIS 4.6 2.0 - - - +
147C ILE* 3.8 29.8 - - + +
150C ALA* 3.7 18.2 - - + -
162C SER 3.2 9.0 + - - +
163C LYS 3.3 6.3 + - - +
165C LEU* 1.3 74.1 - - - +
167C GLN* 1.4 62.6 + - - +
169C ALA* 3.4 6.5 + - - +
170C VAL* 3.2 28.3 + - - +
180C LEU* 4.3 10.2 - - + +
183C ALA* 3.9 33.2 - - + +
184C LEU* 3.8 18.6 - - + +
187C LEU* 3.9 27.1 - - + -
194C LEU* 4.3 10.1 - - + -
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Residues in contact with GLN 167 (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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163C LYS* 2.9 52.4 + - - +
164C GLN* 3.9 11.8 - - - +
166C LEU* 1.4 72.5 - - - +
168C LYS* 1.3 59.0 + - - +
170C VAL* 3.3 9.5 + - - +
171C GLU* 3.0 29.3 + - - +
184C LEU* 4.2 15.8 - - + +
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Residues in contact with LYS 168 (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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126A ASP 5.6 3.3 + - - -
127A ASP* 3.9 21.8 + - - +
129A ARG* 6.4 0.4 - - - +
130A ASP* 3.1 32.3 + - - +
1202A GOL 3.8 15.8 + - - +
136C ARG* 3.6 20.8 - - - +
146C HIS* 5.5 0.7 - - - +
161C LYS* 5.4 1.4 - - - +
164C GLN 2.9 18.4 + - - +
165C LEU* 3.8 6.3 - - - +
167C GLN* 1.3 75.2 - - - +
169C ALA* 1.4 57.6 + - - +
171C GLU* 3.3 16.6 + - - +
172C ARG* 2.9 40.7 + - + +
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Residues in contact with ALA 169 (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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146C HIS* 3.6 38.0 + - + -
165C LEU 3.1 11.0 + - - +
166C LEU 3.5 9.9 - - - +
167C GLN 3.3 0.4 - - - -
168C LYS* 1.4 76.1 - - - +
170C VAL* 1.4 58.3 + - - +
172C ARG* 3.5 2.9 + - - -
173C GLY 3.1 4.5 + - - -
174C ALA* 3.0 32.1 + - + +
180C LEU* 3.7 23.3 - - + +
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Residues in contact with VAL 170 (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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166C LEU 3.2 16.0 + - - +
167C GLN* 3.3 8.5 + - - +
169C ALA* 1.4 73.3 - - - +
171C GLU* 1.3 63.7 + - - +
173C GLY* 3.2 14.0 + - - -
177C LEU* 4.1 22.0 - - + +
180C LEU* 3.8 29.2 - - + -
181C GLU* 4.5 6.7 - - - +
184C LEU* 3.9 20.4 - - + -
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Residues in contact with GLU 171 (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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167C GLN 3.0 17.7 + - - +
168C LYS* 3.5 16.7 - - - +
170C VAL* 1.3 78.7 - - - +
172C ARG* 1.3 72.9 + - - +
173C GLY 3.5 0.9 + - - -
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Residues in contact with ARG 172 (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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124A GLU* 2.8 29.3 + - - +
126A ASP* 3.9 10.4 + - - -
127A ASP* 3.2 34.0 + - - +
1202A GOL 4.1 14.7 - - - +
140C LYS* 3.5 31.1 - - - +
146C HIS* 6.0 1.3 - - + -
168C LYS* 2.9 25.3 + - + +
169C ALA* 4.3 3.6 - - - +
170C VAL 3.3 0.2 - - - -
171C GLU* 1.3 89.2 - - - +
173C GLY* 1.3 62.3 + - - +
174C ALA* 3.6 1.3 - - + +
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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