Contacts of the helix formed by residues 144 - 158 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ASN* 3.0 28.5 + - - +
143A SER* 1.3 81.3 - - - +
145A ARG* 1.3 60.5 + - - +
146A VAL* 3.4 11.6 + - - +
147A PHE* 3.0 21.5 + - - +
148A ARG* 2.9 25.0 + - - +
190A PRO* 6.4 2.2 - - + -
222A ILE* 3.1 10.2 + - + +
223A ALA* 4.4 8.3 - - - +
222B ILE* 5.8 1.0 - - - +
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Residues in contact with ARG 145 (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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144A ASP* 1.3 77.1 - - - +
146A VAL* 1.3 68.3 + - + +
148A ARG* 4.4 6.5 - - - +
149A LEU* 2.8 42.0 + - + +
186A LEU* 3.3 33.7 - - - +
187A PRO* 3.4 17.6 - - - +
188A PHE* 3.0 62.7 + - + +
190A PRO* 4.6 10.0 - - - +
223A ALA* 5.6 0.6 - - - +
224A ASP 6.0 0.8 - - - +
263A PHE* 3.9 26.9 - - + -
264A HIS* 5.6 3.4 - - - +
267A LEU* 5.3 1.8 - - + -
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP* 3.3 11.7 + - - +
145A ARG* 1.3 86.4 - - + +
147A PHE* 1.3 62.9 + - - +
149A LEU* 4.0 6.1 - - + +
150A ALA* 3.2 23.9 + - - +
136B VAL* 5.0 9.0 - - + -
137B CYS* 3.5 27.4 - - + +
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Residues in contact with PHE 147 (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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71A ARG* 6.1 0.9 - - - -
142A ASN* 3.7 26.2 - - - +
143A SER* 4.2 4.3 - - - -
144A ASP* 3.0 20.9 + - - +
146A VAL* 1.3 78.4 - - - +
148A ARG* 1.3 72.3 + - - +
150A ALA* 3.4 4.3 + - - +
151A GLN* 3.1 58.9 + - + +
137B CYS* 3.3 26.6 - - - +
138B ASN 3.8 11.2 - - - -
139B CYS 3.6 15.7 - - - -
140B PRO* 3.6 36.3 - - + -
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Residues in contact with ARG 148 (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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143A SER* 3.4 31.1 + - - +
144A ASP 2.9 9.8 + - - +
145A ARG* 4.1 2.5 - - - +
147A PHE* 1.3 86.0 - - - +
149A LEU* 1.3 61.3 + - - +
151A GLN* 3.0 26.4 + - - +
152A ALA* 2.8 29.5 + - - +
197A GLY* 4.5 4.9 + - - -
219A ARG* 3.8 30.9 + - - +
227A GLN* 3.5 34.1 + - - +
267A LEU* 3.8 26.7 - - + +
268A ASP* 5.0 3.4 + - - +
271A PHE* 3.3 42.9 - - - +
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Residues in contact with LEU 149 (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 ARG* 2.8 29.1 + - + +
146A VAL* 4.0 7.4 - - + +
148A ARG* 1.3 78.6 - - - +
150A ALA* 1.3 57.4 + - - +
152A ALA* 3.2 4.2 + - - +
153A GLN* 2.8 25.1 + - - +
179A TRP* 3.5 18.4 - - + -
182A MSE 3.5 32.1 - - + -
183A HIS* 4.2 12.6 - - + +
186A LEU* 3.7 27.4 - - + -
263A PHE* 4.1 19.5 - - + -
267A LEU* 3.8 11.2 - - + -
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Residues in contact with ALA 150 (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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146A VAL 3.2 15.7 + - - +
147A PHE 3.8 4.0 - - - +
149A LEU* 1.3 79.6 - - - +
151A GLN* 1.3 61.2 + - - +
153A GLN* 3.4 9.0 + - - +
154A SER* 3.2 26.5 + - - -
137B CYS* 3.8 33.2 - - + +
138B ASN* 5.6 2.0 - - - +
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Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 5.8 1.6 + - - -
147A PHE* 3.1 44.2 + - + +
148A ARG* 3.0 36.4 + - - +
150A ALA* 1.3 74.6 - - - +
152A ALA* 1.3 58.3 + - - +
154A SER* 3.3 7.0 + - - -
155A ARG* 3.0 32.9 + - + +
219A ARG* 6.0 0.7 - - - +
271A PHE* 3.4 16.9 - - + -
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Residues in contact with ALA 152 (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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148A ARG 2.8 17.0 + - - +
149A LEU 3.2 5.8 + - - +
151A GLN* 1.3 74.1 - - - +
153A GLN* 1.3 66.4 + - - +
155A ARG* 3.3 4.6 + - - +
156A MSE 2.9 25.8 + - - +
179A TRP* 4.0 11.0 - - + -
267A LEU* 4.1 8.5 - - + -
270A PHE* 3.7 34.6 - - + -
271A PHE* 3.8 11.4 - - + -
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Residues in contact with GLN 153 (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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149A LEU 2.8 16.5 + - - +
150A ALA* 3.7 9.0 - - - +
151A GLN 3.3 0.2 - - - -
152A ALA* 1.3 77.2 - - - +
154A SER* 1.3 59.0 + - - +
156A MSE 3.3 12.4 + - + +
157A ASN* 2.9 51.4 + - - +
179A TRP* 3.6 39.1 - - + +
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Residues in contact with SER 154 (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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150A ALA 3.2 15.4 + - - -
151A GLN* 3.7 6.5 - - - -
152A ALA 3.2 0.2 - - - -
153A GLN* 1.3 76.4 - - - +
155A ARG* 1.3 59.3 + - - +
157A ASN* 3.2 7.5 + - - +
158A ASN* 2.8 46.3 + - - +
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Residues in contact with ARG 155 (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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151A GLN* 3.0 17.4 + - + +
152A ALA 3.3 4.5 + - - +
154A SER* 1.3 75.4 - - - +
156A MSE 1.3 61.1 + - - +
158A ASN* 3.4 3.0 + - - +
159A GLY 3.1 3.5 + - - -
160A LEU* 2.8 79.7 + - + +
161A VAL* 3.8 6.2 + - + +
162A ASP 5.0 1.6 - - - +
219A ARG* 6.0 1.1 - - - -
270A PHE 2.6 33.0 + - - +
271A PHE* 3.8 44.7 + - - +
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Residues in contact with MSE 156 (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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152A ALA 2.9 12.4 + - - +
153A GLN* 3.5 16.2 - - + +
155A ARG* 1.3 75.4 - - - +
157A ASN* 1.3 78.4 + - - +
159A GLY* 3.1 13.7 + - - -
160A LEU 4.9 0.2 - - - +
161A VAL* 3.7 16.9 - - + +
175A VAL* 3.8 33.8 - - + +
176A GLU* 4.3 16.6 - - - +
179A TRP* 3.6 56.5 - - + +
270A PHE* 4.2 3.8 - - + -
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Residues in contact with ASN 157 (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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153A GLN* 2.9 39.2 + - - +
154A SER* 3.7 8.1 - - - +
156A MSE 1.3 91.6 - - - +
158A ASN* 1.3 63.2 + - - +
159A GLY 3.2 1.4 + - - -
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Residues in contact with ASN 158 (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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154A SER* 2.8 30.7 + - - +
156A MSE 3.2 0.2 - - - -
157A ASN* 1.3 79.2 - - - +
159A GLY* 1.3 60.3 + - - +
160A LEU* 3.3 33.5 - - + +
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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