Contacts of the helix formed by residues 162 - 177 (chain B) in PDB entry 4KAL
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B VAL 4.9 2.2 + - - +
134B GLU* 3.5 19.6 + - - +
135B LEU 3.6 9.4 + - - +
136B GLY* 3.9 7.8 - - - -
137B PRO* 3.8 8.7 - - - +
138B GLU* 2.6 43.4 + - - -
160B PRO* 3.5 0.4 - - - +
161B PRO* 1.3 93.8 - - + +
163B ALA* 1.3 66.1 + - - +
164B LYS 3.2 2.7 - - - -
165B GLU* 3.1 45.7 + - - +
166B ALA 3.6 2.6 + - - -
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.4 26.2 + - + +
157B LEU* 3.5 43.7 - - + +
160B PRO* 4.1 12.0 + - + +
161B PRO 3.6 1.4 - - - -
162B ARG* 1.3 78.2 - - - +
164B LYS* 1.3 62.9 + - - +
166B ALA* 3.0 18.8 + - - +
167B ILE* 3.0 15.7 + - - +
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Residues in contact with LYS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU 4.2 4.0 + - - +
158B TRP* 3.6 76.6 + - + +
160B PRO 4.2 4.6 + - - -
161B PRO* 3.6 23.9 + - - +
163B ALA* 1.3 77.4 - - - +
165B GLU* 1.3 66.4 + - + +
167B ILE* 3.2 2.9 + - - +
168B LEU* 2.9 38.3 + - + +
194B TYR* 5.9 0.6 - - - -
197B GLU* 4.0 8.5 - - - +
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PRO* 3.5 26.7 - - + +
161B PRO 4.5 1.7 - - - +
162B ARG* 3.1 42.1 + - - +
164B LYS* 1.3 82.9 - - + +
166B ALA* 1.3 64.6 + - - +
168B LEU* 3.4 8.8 + - - +
169B ASP* 3.1 27.5 + - - +
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 5.7 2.5 - - + -
135B LEU* 5.2 8.7 - - + -
136B GLY* 3.7 28.0 - - - +
137B PRO* 4.1 6.5 - - - +
139B ASP 5.9 0.2 - - - -
140B VAL* 3.6 17.3 - - + +
162B ARG 3.6 2.0 + - - -
163B ALA* 3.0 13.2 + - - +
165B GLU* 1.3 77.8 - - - +
167B ILE* 1.3 62.3 + - + +
169B ASP* 3.2 4.6 + - - +
170B CYS* 2.9 33.1 + - - -
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 3.7 29.8 - - + -
151B THR* 6.0 0.7 - - + -
153B PHE* 3.6 62.6 - - + -
157B LEU* 3.8 12.8 - - + -
158B TRP* 3.9 17.7 - - + -
163B ALA 3.0 13.0 + - - +
164B LYS 3.2 7.2 + - - +
166B ALA* 1.3 76.4 - - + +
168B LEU* 1.3 64.5 + - + +
170B CYS* 3.2 9.6 + - + +
171B ALA* 2.9 28.5 + - + +
181B MSE 4.5 2.8 - - + +
201B LEU* 5.5 1.3 - - + -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B TRP* 5.3 4.5 - - + -
164B LYS* 2.9 26.6 + - + +
165B GLU* 3.9 7.6 - - - +
167B ILE* 1.3 78.3 - - + +
169B ASP* 1.3 62.4 + - - +
171B ALA* 3.4 5.6 + - + +
172B ARG* 3.1 31.3 + - - +
201B LEU* 4.3 14.8 - - + -
206B LYS* 3.7 36.3 - - + -
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Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PRO* 3.4 30.7 - - - +
140B VAL* 4.4 13.0 - - + +
165B GLU 3.1 15.1 + - - +
166B ALA 3.2 8.7 + - - +
168B LEU* 1.3 74.0 - - - +
170B CYS* 1.3 63.5 + - - +
172B ARG* 2.6 39.8 + - - +
173B ILE* 3.1 32.8 + - + +
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Residues in contact with CYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 4.6 7.2 - - - -
76B PHE* 4.3 12.3 - - - -
140B VAL* 4.1 13.9 - - - -
145B VAL* 3.4 30.1 - - + +
151B THR* 4.2 23.3 - - + -
166B ALA* 2.9 21.1 + - - -
167B ILE* 3.2 14.1 + - + +
169B ASP* 1.3 74.8 - - - +
171B ALA* 1.3 53.8 + - - +
173B ILE* 3.3 1.4 + - - -
174B ALA* 2.8 37.2 + - - +
181B MSE 4.1 4.7 - - + -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ILE* 2.9 14.5 + - + +
168B LEU* 3.6 12.3 - - + +
169B ASP 3.3 0.2 - - - -
170B CYS* 1.3 73.4 - - - +
172B ARG* 1.3 64.7 + - - +
174B ALA* 3.8 0.3 - - - +
175B HIS* 3.0 33.3 + - - +
181B MSE 3.7 18.1 - - + -
206B LYS* 4.2 36.8 - - + +
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Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 3.1 20.9 + - - +
169B ASP* 2.6 42.4 + - - +
171B ALA* 1.3 77.2 - - - +
173B ILE* 1.3 63.6 + - - +
175B HIS* 3.9 2.1 - - - +
176B GLN* 2.9 56.8 + - + +
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL* 4.0 19.7 - - + -
142B ALA* 3.7 32.5 - - + +
145B VAL* 3.8 5.6 - - + -
146B ALA* 3.7 26.0 - - + +
169B ASP* 3.1 21.9 + - + +
170B CYS 3.9 2.2 - - - +
172B ARG* 1.3 78.5 - - + +
174B ALA* 1.3 66.5 + - - +
176B GLN* 3.3 10.1 + - - +
177B HIS* 3.1 42.0 + - + +
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B VAL* 3.7 13.6 - - + +
151B THR* 4.7 2.7 - - - +
170B CYS 2.8 22.3 + - - +
171B ALA 3.8 0.9 - - - +
173B ILE* 1.3 74.1 - - - +
175B HIS* 1.3 62.3 + - - +
177B HIS 3.1 8.1 + - - -
178B GLY 3.1 0.2 + - - -
179B ARG* 2.8 48.5 + - + +
180B GLU 4.7 1.8 - - - +
181B MSE 3.6 26.5 - - + -
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Residues in contact with HIS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ALA* 3.0 20.0 + - + +
172B ARG* 4.1 2.0 - - - +
174B ALA* 1.3 77.2 - - - +
176B GLN* 1.3 64.5 + - - +
178B GLY* 3.1 12.9 + - - -
179B ARG 3.3 20.4 - - - -
181B MSE 3.6 10.0 - - + +
205B GLY 3.1 27.1 + - - -
206B LYS* 3.4 22.1 - - - +
208B ASP* 2.7 27.2 + - - -
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Residues in contact with GLN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ARG* 2.9 44.5 + - + +
173B ILE* 3.7 9.3 - - - +
175B HIS* 1.3 76.7 - - - +
177B HIS* 1.3 71.5 + - + +
178B GLY 3.3 1.0 + - - -
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Residues in contact with HIS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA* 3.6 46.5 - - + +
147B ASP* 5.6 0.9 - - - -
173B ILE* 3.1 29.9 + - + +
174B ALA 3.1 5.1 + - - +
176B GLN* 1.3 89.3 - - + +
178B GLY* 1.3 61.2 + - - +
179B ARG* 3.3 22.4 + - + +
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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