Contacts of the helix formed by residues 162 - 177 (chain A) in PDB entry 4K8T
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 ARG 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A VAL 5.4 2.2 - - - +
134A GLU 5.8 0.6 + - - -
135A LEU 3.5 15.2 + - - +
136A GLY* 3.9 6.0 - - - -
137A PRO* 3.8 12.9 - - - +
138A GLU* 3.8 24.2 + - - -
160A PRO* 5.0 0.2 - - - +
161A PRO* 1.3 94.3 - - + +
163A ALA* 1.3 66.3 + - - +
164A LYS 3.2 2.7 - - - -
165A GLU* 2.8 58.1 + - - +
166A ALA 3.5 3.5 + - - -
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Residues in contact with ALA 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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135A LEU* 3.4 24.8 + - + +
157A LEU* 3.3 46.7 - - + +
160A PRO* 4.1 12.2 + - + +
161A PRO 3.7 1.2 - - - -
162A ARG* 1.3 76.8 - - - +
164A LYS* 1.3 63.1 + - - +
166A ALA* 3.0 18.0 + - - +
167A ILE* 3.1 16.7 + - - +
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Residues in contact with LYS 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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157A LEU 4.3 3.4 + - - +
158A TRP* 3.6 72.7 + - + +
160A PRO 5.2 1.8 + - - +
161A PRO 4.1 19.0 - - - +
163A ALA* 1.3 77.4 - - - +
165A GLU* 1.3 66.1 + - + +
167A ILE* 3.3 3.3 + - - +
168A LEU* 3.0 37.5 + - + +
194A TYR* 5.5 3.2 - - - -
197A GLU* 4.6 13.1 + - - +
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Residues in contact with GLU 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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137A PRO* 3.5 13.6 - - + +
161A PRO 4.7 1.6 - - - +
162A ARG* 2.8 65.5 + - - +
164A LYS* 1.3 82.9 - - + +
166A ALA* 1.3 64.6 + - - +
168A LEU* 3.5 10.1 + - + +
169A ASP* 3.1 27.0 + - - +
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Residues in contact with ALA 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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7A VAL* 5.8 2.5 - - + -
135A LEU* 5.2 8.3 - - + -
136A GLY* 3.7 28.5 - - - +
137A PRO* 4.0 6.3 - - - +
139A ASP 5.9 0.2 - - - -
140A VAL* 3.7 18.0 - - + +
162A ARG 3.5 2.2 + - - -
163A ALA* 3.0 12.8 + - - +
165A GLU* 1.3 77.4 - - - +
167A ILE* 1.3 61.6 + - + +
169A ASP* 3.2 5.9 + - - +
170A CYS* 2.8 33.2 + - - -
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Residues in contact with ILE 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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7A VAL* 3.7 20.0 - - + -
151A THR* 6.1 0.4 - - + -
153A PHE* 3.6 60.3 - - + -
157A LEU* 3.7 22.4 - - + -
158A TRP* 3.8 18.2 - - + -
163A ALA 3.1 13.5 + - - +
164A LYS 3.5 7.6 - - - +
165A GLU 3.2 0.2 - - - -
166A ALA* 1.3 75.2 - - + +
168A LEU* 1.3 55.6 + - + +
170A CYS* 3.0 11.2 + - + +
171A ALA* 2.8 32.8 + - + +
181A MSE 4.2 3.3 - - + +
201A LEU* 5.2 4.5 - - + -
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Residues in contact with LEU 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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158A TRP* 5.5 3.4 - - + -
164A LYS* 3.0 26.5 + - + +
165A GLU* 3.9 8.5 - - + +
166A ALA 3.4 0.2 - - - -
167A ILE* 1.3 72.7 - - + +
169A ASP* 1.3 67.1 + - - +
171A ALA* 3.3 6.5 + - + +
172A ARG* 3.1 24.4 + - - +
201A LEU* 4.3 15.9 - - + -
206A LYS* 3.7 34.8 - - + -
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Residues in contact with ASP 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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137A PRO* 3.2 31.5 - - - +
140A VAL* 4.3 12.3 - - + -
165A GLU 3.1 12.3 + - - +
166A ALA 3.4 8.5 - - - +
168A LEU* 1.3 79.5 - - - +
170A CYS* 1.3 61.0 + - - +
172A ARG* 3.4 26.1 + - - +
173A ILE* 3.1 32.8 + - + +
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Residues in contact with CYS 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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7A VAL* 4.7 6.7 - - - -
76A PHE* 4.3 13.2 - - - -
140A VAL* 3.9 13.9 - - - -
145A VAL* 3.4 29.1 - - + +
151A THR* 4.4 21.1 - - + -
166A ALA* 2.8 24.8 + - - -
167A ILE* 3.0 13.9 + - + +
169A ASP* 1.3 70.1 - - - +
171A ALA* 1.3 55.9 + - - +
173A ILE* 3.4 0.6 + - - -
174A ALA* 2.8 37.8 + - - +
181A MSE 4.0 5.4 - - + -
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Residues in contact with ALA 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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167A ILE* 2.8 16.3 + - + +
168A LEU* 3.5 13.9 - - + +
169A ASP 3.3 0.2 - - - -
170A CYS* 1.3 72.1 - - - +
172A ARG* 1.3 57.9 + - - +
174A ALA* 3.8 0.7 - - - +
175A HIS* 3.0 39.9 + - - +
181A MSE 3.7 21.1 - - + +
201A LEU* 6.4 0.2 - - + -
206A LYS* 4.1 33.2 - - + +
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Residues in contact with ARG 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 LEU 3.1 12.0 + - - +
169A ASP* 3.4 37.3 + - - +
171A ALA* 1.3 80.8 - - - +
173A ILE* 1.3 76.0 + - - +
175A HIS* 4.0 2.7 - - - +
176A GLN* 2.9 63.9 + - + +
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Residues in contact with ILE 173 (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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140A VAL* 4.2 16.2 - - + -
142A ALA* 3.7 36.6 - - + +
145A VAL* 3.8 7.9 - - + -
146A ALA* 3.7 28.5 - - + +
169A ASP* 3.1 20.5 + - + +
172A ARG* 1.3 93.0 - - - +
174A ALA* 1.3 66.6 + - - +
176A GLN* 3.4 6.2 + - - -
177A HIS* 3.1 39.0 + - + +
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Residues in contact with ALA 174 (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 VAL* 3.6 14.7 - - + +
151A THR* 4.7 3.8 - - - +
170A CYS 2.8 19.1 + - - +
171A ALA 3.8 1.1 - - - +
173A ILE* 1.3 76.6 - - - +
175A HIS* 1.3 57.1 + - - +
177A HIS 3.1 8.3 + - - -
178A GLY 3.2 0.2 + - - -
179A ARG* 2.8 49.7 + - + +
180A GLU 4.7 2.2 - - - +
181A MSE 3.6 26.5 - - + -
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Residues in contact with HIS 175 (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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171A ALA* 3.0 25.1 + - - +
172A ARG* 4.1 2.9 - - - +
174A ALA* 1.3 73.9 - - - +
176A GLN* 1.3 66.8 + - + +
178A GLY* 3.1 13.2 + - - -
179A ARG 3.7 17.9 - - - -
181A MSE 3.7 8.9 - - + +
205A GLY 3.0 26.9 + - - -
206A LYS* 3.5 25.0 - - - +
208A ASP* 3.0 26.1 + - - -
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Residues in contact with GLN 176 (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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172A ARG* 2.9 51.7 + - + +
173A ILE* 4.0 5.6 - - - +
174A ALA 3.3 0.2 - - - -
175A HIS* 1.3 77.4 - - + +
177A HIS* 1.3 67.9 + - + +
178A GLY 3.3 1.0 + - - -
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Residues in contact with HIS 177 (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 ALA* 3.6 46.0 - - + +
147A ASP* 5.6 0.9 - - - -
173A ILE* 3.1 32.3 + - + +
174A ALA 3.1 3.1 + - - +
176A GLN* 1.3 84.5 - - + +
178A GLY* 1.3 61.3 + - - +
179A ARG* 3.3 22.5 + - + +
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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