Contacts of the helix formed by residues 144 - 158 (chain C) in PDB entry 4GKH
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 144 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C ASN* 3.0 27.2 + - - +
143C SER* 1.3 80.6 - - - +
145C ARG* 1.3 61.5 + - - +
146C VAL* 3.4 13.9 + - - +
147C PHE* 3.0 20.9 + - - +
148C ARG* 2.8 25.7 + - - +
192C SER* 6.1 0.7 - - - +
222C ILE* 3.2 11.1 + - + +
223C ALA* 4.3 9.0 - - - +
222D ILE* 6.1 0.2 - - - +
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Residues in contact with ARG 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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144C ASP* 1.3 77.9 - - - +
146C VAL* 1.3 69.6 + - + +
148C ARG* 4.3 7.9 - - - +
149C LEU* 2.8 41.0 + - + +
186C LEU* 3.4 33.2 - - - +
187C PRO* 4.1 12.9 - - - +
188C PHE* 3.4 57.9 + - + +
189C SER 5.2 2.2 - - - -
190C PRO* 5.2 4.2 - - - +
223C ALA* 5.4 0.6 - - - +
224C ASP* 6.0 1.2 - - + +
263C PHE* 4.0 24.2 - - + -
264C HIS* 5.4 4.5 - - - +
267C LEU* 5.2 2.2 - - + -
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Residues in contact with VAL 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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144C ASP* 3.2 12.7 + - - +
145C ARG* 1.3 88.9 - - + +
147C PHE* 1.3 62.3 + - - +
149C LEU* 3.9 8.0 - - + +
150C ALA* 3.3 16.8 + - - +
136D VAL* 5.1 8.3 - - + -
137D CYS* 3.5 33.7 - - + +
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Residues in contact with PHE 147 (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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71C ARG* 5.9 1.8 - - - -
142C ASN* 3.7 26.0 - - - +
143C SER* 4.0 5.6 - - - -
144C ASP* 3.0 21.4 + - - +
146C VAL* 1.3 76.2 - - - +
148C ARG* 1.3 79.0 + - - +
150C ALA 3.3 1.4 + - - -
151C GLN* 3.1 60.2 + - + +
137D CYS* 3.4 25.7 - - - +
138D ASN* 3.7 12.1 - - - -
139D CYS 3.7 15.5 - - - -
140D PRO* 3.7 34.5 - - + -
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Residues in contact with ARG 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C SER* 3.3 33.4 + - - +
144C ASP 2.8 14.6 + - - +
145C ARG* 4.1 2.0 - - - +
147C PHE* 1.3 83.0 - - - +
149C LEU* 1.3 60.9 + - - +
151C GLN* 3.1 24.6 + - - +
152C ALA* 2.8 29.6 + - - +
197C GLY* 4.4 4.2 + - - -
219C ARG* 3.9 29.2 + - - +
227C GLN* 3.3 36.1 + - - +
267C LEU* 3.8 29.0 - - + +
268C ASP* 5.0 3.4 + - - -
271C PHE* 3.3 44.0 - - - +
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Residues in contact with LEU 149 (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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145C ARG* 2.8 36.4 + - + +
146C VAL* 3.9 7.6 - - + +
148C ARG* 1.3 73.5 - - - +
150C ALA* 1.3 59.0 + - - +
152C ALA* 3.3 2.1 + - - +
153C GLN 2.8 24.6 + - - -
179C TRP* 3.5 22.2 - - + -
182C MSE 3.5 32.5 - - + -
183C HIS* 4.2 10.3 - - + +
186C LEU* 3.9 26.5 - - + -
263C PHE* 4.1 20.2 - - + -
267C LEU* 4.1 9.9 - - + -
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Residues in contact with ALA 150 (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 VAL 3.3 12.3 + - - +
147C PHE 3.8 0.2 - - - +
148C ARG 3.2 0.2 - - - -
149C LEU* 1.3 76.0 - - - +
151C GLN* 1.3 66.1 + - - +
153C GLN* 3.4 10.8 + - - +
154C SER* 3.1 26.5 + - - -
137D CYS* 3.6 41.7 - - - +
138D ASN* 5.3 3.8 - - - +
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Residues in contact with GLN 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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67C ASP* 5.8 2.0 + - - -
147C PHE* 3.1 48.9 + - + +
148C ARG* 3.1 35.2 + - - +
150C ALA* 1.3 77.4 - - - +
152C ALA* 1.3 56.6 + - - +
154C SER* 3.3 7.2 + - - -
155C ARG* 2.9 32.2 + - + +
219C ARG* 6.1 0.3 - - - +
271C PHE* 3.4 17.8 - - + -
137D CYS 5.8 0.2 - - - +
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Residues in contact with ALA 152 (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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148C ARG 2.8 19.6 + - - +
149C LEU 3.3 5.4 + - - +
151C GLN* 1.3 71.1 - - - +
153C GLN* 1.3 65.3 + - - +
155C ARG* 3.3 4.8 + - - +
156C MSE 2.9 24.8 + - - +
179C TRP* 4.1 10.3 - - + -
267C LEU* 4.0 16.2 - - + -
270C PHE* 3.7 33.8 - - + -
271C PHE* 3.8 6.9 - - + -
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Residues in contact with GLN 153 (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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149C LEU 2.8 17.5 + - - +
150C ALA* 3.7 11.3 - - - +
151C GLN 3.3 0.2 - - - -
152C ALA* 1.3 76.0 - - - +
154C SER* 1.3 58.9 + - - +
156C MSE 3.3 11.5 + - + +
157C ASN* 2.8 51.2 + - - +
179C TRP* 3.6 35.0 - - + +
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Residues in contact with SER 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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150C ALA 3.1 14.4 + - - -
151C GLN* 3.7 8.5 - - - -
153C GLN* 1.3 74.2 - - - +
155C ARG* 1.3 60.6 + - - +
157C ASN* 3.6 6.2 - - - +
158C ASN* 2.8 48.8 + - - +
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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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36C SER* 6.4 0.4 - - - +
151C GLN* 2.9 22.2 + - + +
152C ALA 3.7 4.9 - - - +
154C SER* 1.3 75.1 - - - +
156C MSE 1.3 61.3 + - - +
159C GLY 3.3 3.5 + - - -
160C LEU* 2.9 84.4 + - + +
161C VAL* 3.7 7.3 + - + +
162C ASP 5.1 1.2 - - - +
270C PHE 3.0 31.5 + - - +
271C PHE* 3.7 39.2 + - + -
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Residues in contact with MSE 156 (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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152C ALA 2.9 12.4 + - - +
153C GLN* 3.5 15.0 - - + +
155C ARG* 1.3 77.6 - - - +
157C ASN* 1.3 78.1 + - - +
159C GLY* 3.1 15.1 + - - -
161C VAL* 3.6 12.4 - - + +
175C VAL* 3.7 37.0 - - + +
176C GLU* 4.1 19.1 - - + +
179C TRP* 3.7 55.4 - - + +
270C PHE* 4.3 3.4 - - + -
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Residues in contact with ASN 157 (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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153C GLN* 2.8 42.5 + - - +
154C SER* 3.8 6.8 - - - +
156C MSE 1.3 91.2 - - - +
158C ASN* 1.3 63.5 + - - +
159C GLY 3.2 0.9 + - - -
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Residues in contact with ASN 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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154C SER* 2.8 37.3 + - - +
157C ASN* 1.3 74.5 - - - +
159C GLY* 1.3 60.9 + - - +
160C LEU* 3.6 31.1 - - + +
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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