Contacts of the helix formed by residues 150 - 165 (chain C) in PDB entry 5G04
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 ALA 150 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C ARG* 3.8 15.3 - - + +
123C TYR* 4.6 3.6 - - - +
126C GLY* 3.6 16.6 - - - -
129C LYS* 5.8 2.5 - - + +
148C ASN* 3.1 16.9 - - - +
149C GLU* 1.3 75.5 - - - +
151C LEU* 1.3 58.4 + - + +
152C ARG 3.4 1.3 - - - -
153C GLU* 3.6 14.0 + - - +
154C LEU* 2.9 42.7 + - + +
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Residues in contact with LEU 151 (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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123C TYR* 3.7 20.0 - - + -
148C ASN* 3.6 30.5 - - + +
149C GLU 3.4 3.1 - - - +
150C ALA* 1.3 78.0 - - - +
152C ARG* 1.3 66.4 + - - +
154C LEU* 3.2 4.1 + - + +
155C ARG* 3.0 24.9 + - - +
178C VAL* 3.5 42.9 - - + +
181C LYS* 3.0 35.9 - - + +
182C LEU* 3.6 23.7 - - + +
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Residues in contact with ARG 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C GLU* 4.8 9.7 - - + +
150C ALA 3.4 1.4 - - - +
151C LEU* 1.3 79.3 - - - +
153C GLU* 1.3 79.4 + - + +
155C ARG* 3.6 23.4 + - - +
156C VAL* 3.4 28.9 - - - +
182C LEU* 4.5 8.6 - - + +
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Residues in contact with GLU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ARG* 5.7 2.3 + - - +
149C GLU 3.0 24.5 - - - +
150C ALA* 3.6 12.2 + - - +
151C LEU 3.3 0.4 - - - -
152C ARG* 1.3 93.8 - - + +
154C LEU* 1.3 61.3 + - + +
156C VAL* 3.2 14.0 + - - +
157C GLU* 2.4 39.5 - - - +
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Residues in contact with LEU 154 (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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119C MET* 4.1 7.2 - - + +
122C ARG* 3.9 35.0 - - + +
123C TYR* 3.7 36.1 - - + +
150C ALA* 2.9 36.0 + - + +
151C LEU* 3.2 8.5 + - + +
153C GLU* 1.3 78.2 - - + +
155C ARG* 1.3 55.1 + - - +
157C GLU* 3.2 8.5 + - + +
158C LEU* 2.8 55.5 + - + +
174C LEU* 4.8 2.5 - - + -
178C VAL* 4.0 20.4 - - + -
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Residues in contact with ARG 155 (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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151C LEU 3.0 15.3 + - - +
152C ARG* 3.7 19.8 - - - +
154C LEU* 1.3 76.1 - - - +
156C VAL* 1.3 54.5 + - + +
158C LEU* 4.0 3.3 - - - +
159C SER* 2.8 39.6 + - - -
175C TYR* 4.2 11.0 - - + +
178C VAL* 4.1 7.6 - - + +
179C LEU* 5.8 2.9 - - + -
182C LEU* 4.1 26.8 - - + +
184C LEU* 3.8 30.2 - - + +
187C GLU* 5.3 4.8 + - - -
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ARG* 3.4 28.7 - - - +
153C GLU* 3.4 9.9 - - - +
155C ARG* 1.3 75.4 - - + +
157C GLU* 1.3 71.0 + - - +
159C SER* 2.7 21.9 + - - +
160C LYS* 3.2 10.7 + - - +
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Residues in contact with GLU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C MET* 3.5 27.6 - - + -
122C ARG* 3.6 18.4 + - - -
153C GLU* 2.4 40.4 - - - +
154C LEU* 3.3 16.7 + - - +
156C VAL* 1.3 82.5 - - - +
158C LEU* 1.3 62.0 + - - +
160C LYS* 3.2 25.3 + - - +
161C LYS* 3.2 22.1 + - - +
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Residues in contact with LEU 158 (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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115C TYR* 4.1 9.9 - - - +
119C MET* 3.7 31.4 - - + -
154C LEU* 2.8 41.3 + - + +
155C ARG* 4.0 0.7 - - - +
157C GLU* 1.3 79.2 - - - +
159C SER* 1.3 55.6 + - - +
161C LYS* 3.2 7.1 + - - +
162C HIS* 2.9 29.8 + - - +
167C LEU* 3.7 29.8 - - + +
171C GLY 4.4 0.4 - - - +
174C LEU* 3.8 24.5 - - + -
175C TYR* 3.5 30.6 - - + -
178C VAL* 5.2 3.4 - - + -
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Residues in contact with SER 159 (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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155C ARG* 2.8 22.6 + - - -
156C VAL* 2.7 25.5 + - - +
158C LEU* 1.3 69.7 - - - +
160C LYS* 1.3 59.6 + - - +
162C HIS* 3.3 2.0 + - - +
163C GLN* 2.9 43.9 + - - +
175C TYR* 3.6 25.2 - - - -
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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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156C VAL 3.2 7.8 + - - +
157C GLU* 3.2 20.4 + - - +
159C SER* 1.3 81.9 + - - +
161C LYS* 1.3 85.6 - - - +
163C GLN* 3.4 11.9 + - - +
164C ALA* 3.1 23.1 + - + +
166C GLU* 5.1 4.4 + - - -
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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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115C TYR* 1.6 79.8 - - + +
118C TYR* 5.3 2.2 - - - -
119C MET* 3.3 17.0 - - - +
157C GLU* 3.2 17.5 + - - +
158C LEU* 3.2 8.4 + - - +
160C LYS* 1.3 92.0 - - - +
162C HIS* 1.3 59.2 + - - +
164C ALA* 3.3 2.6 + - - +
165C ARG 2.9 22.9 + - - -
166C GLU* 3.4 34.2 + - + +
167C LEU* 4.0 13.1 + - + -
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Residues in contact with HIS 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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158C LEU 2.9 17.7 + - - +
159C SER 3.6 5.2 + - - +
161C LYS* 1.3 76.8 - - - +
163C GLN* 1.3 64.7 + - + +
165C ARG* 3.0 26.7 + - + +
167C LEU* 4.6 13.1 - - + +
172C LEU* 3.6 26.5 - - + +
175C TYR* 3.4 35.1 + + + -
191C VAL* 4.5 11.0 - - + +
194C GLU* 5.4 6.5 - - - +
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Residues in contact with GLN 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 SER* 2.9 31.2 + - - +
160C LYS* 3.8 9.4 - - - +
162C HIS* 1.3 83.0 - - + +
164C ALA* 1.3 61.1 + - - +
165C ARG* 3.4 8.5 + - - +
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Residues in contact with ALA 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* 3.1 13.6 + - + +
161C LYS 3.5 5.2 - - - +
162C HIS 3.2 0.2 - - - -
163C GLN* 1.3 75.8 - - - +
165C ARG* 1.3 68.2 + - - +
166C GLU* 3.3 28.3 + - + +
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Residues in contact with ARG 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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161C LYS 2.9 5.5 + - - -
162C HIS* 3.0 20.3 + - + +
163C GLN 3.9 6.7 - - - +
164C ALA* 1.3 80.6 - - - +
166C GLU* 1.3 63.8 + - - +
167C LEU 3.4 12.5 + - - +
168C ASP* 5.5 5.4 + - - +
172C LEU* 6.2 1.6 - - - +
194C GLU* 4.6 14.8 + - - -
198C VAL* 5.2 8.9 - - - +
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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