Contacts of the helix formed by residues 153 - 172 (chain A) in PDB entry 3K3T
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A SO4 2.9 30.5 + - - +
154A GLN* 1.3 67.8 + - - +
155A ALA 3.3 2.9 - - - +
156A PHE* 3.2 9.1 + - - +
157A VAL* 3.0 23.8 + - - +
188A TRP* 3.7 38.1 - - + -
190A LYS* 6.5 0.4 - - + -
303A ARG* 3.6 23.6 - - - +
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Residues in contact with GLN 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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1A SO4 3.0 18.2 + - - +
153A ALA* 1.3 78.0 - - - +
155A ALA* 1.3 58.8 + - - +
157A VAL* 3.3 7.1 + - - +
158A ASP* 2.8 62.4 + - - +
303A ARG* 2.9 51.0 + - - +
306A ALA* 3.5 15.5 - - + +
307A SER* 3.5 9.9 - - - +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA 3.3 0.6 - - - +
154A GLN* 1.3 76.0 - - - +
156A PHE* 1.3 60.6 + - - +
158A ASP* 3.8 7.8 - - - +
159A ALA* 2.9 33.2 + - - +
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Residues in contact with PHE 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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153A ALA* 3.2 12.9 + - - +
155A ALA* 1.3 78.4 - - - +
157A VAL* 1.3 68.1 + - + +
159A ALA* 3.9 3.4 - - - +
160A THR* 2.9 49.2 + - + +
179A VAL* 4.6 4.7 - - + -
182A ALA* 3.9 21.5 - - + -
183A ALA* 3.9 24.5 - - + -
186A THR* 3.5 22.9 - - - -
188A TRP* 3.8 24.9 - + - +
189A GLY* 3.5 15.3 - - - -
192A GLN* 4.1 14.6 - - - -
204A LEU* 4.1 10.1 - - + -
243A TYR* 4.0 13.5 - - - -
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA 3.0 16.5 + - - +
154A GLN* 3.6 12.3 - - - +
156A PHE* 1.3 80.2 - - + +
158A ASP* 1.3 56.2 + - - +
160A THR* 3.3 6.5 + - - -
161A TRP* 3.0 32.2 + - + +
179A VAL* 4.3 14.5 - - + +
188A TRP* 3.8 30.7 - - + -
300A LEU* 5.0 0.9 - - + -
303A ARG* 4.1 34.3 - - + +
304A LEU* 4.4 15.7 - - + -
307A SER* 4.3 8.7 - - - +
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Residues in contact with ASP 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 GLN* 2.8 44.3 + - - +
155A ALA* 3.8 7.2 - - - +
157A VAL* 1.3 73.0 - - - +
159A ALA* 1.3 62.4 + - - +
161A TRP* 3.9 2.4 - - - +
162A PRO* 3.4 18.7 - - - +
307A SER* 2.8 32.3 + - - +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA 2.9 18.6 + - - +
156A PHE* 3.9 4.0 - - - +
158A ASP* 1.3 76.3 - - - +
160A THR* 1.3 61.8 + - - +
162A PRO* 3.5 10.8 - - - +
163A GLN* 4.2 11.6 + - - +
243A TYR* 4.3 26.2 - - + +
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Residues in contact with THR 160 (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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156A PHE* 2.9 36.9 + - + +
157A VAL* 3.3 9.0 + - - -
159A ALA* 1.3 76.5 - - - +
161A TRP* 1.3 62.2 + - - +
163A GLN* 3.1 6.4 + - - +
164A ALA* 2.8 28.6 + - - +
179A VAL* 4.1 17.3 - - - +
182A ALA* 5.7 0.4 - - - -
204A LEU* 3.5 28.9 - - + -
243A TYR* 4.4 12.3 - - + -
247A PHE* 4.1 17.4 - - + -
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Residues in contact with TRP 161 (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 VAL* 3.0 19.7 + - + +
158A ASP 3.9 4.5 - - - +
160A THR* 1.3 76.3 + - - +
162A PRO* 1.4 72.3 - - + +
164A ALA* 3.2 4.8 + - - +
165A ALA* 2.8 38.7 + - + +
175A ALA* 3.6 28.9 - - + -
176A HIS* 4.1 11.9 - - + -
179A VAL* 4.1 11.2 - - + -
304A LEU* 3.6 33.4 - - + -
307A SER* 4.6 13.5 - - - +
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Residues in contact with PRO 162 (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 ASP 3.4 17.3 - - - +
159A ALA* 3.5 12.6 - - - +
161A TRP* 1.4 101.1 - - + +
163A GLN* 1.3 68.8 + - - +
165A ALA* 3.5 5.4 + - + +
166A LYS* 3.0 33.5 + - - +
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Residues in contact with GLN 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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159A ALA 4.2 15.0 + - - +
160A THR 3.1 3.3 + - - +
162A PRO* 1.3 82.9 - - - +
164A ALA* 1.3 61.8 + - - +
166A LYS* 3.1 35.4 + - - +
167A ALA* 3.0 30.3 + - - +
243A TYR* 4.2 5.2 - - + -
244A GLU* 3.5 45.4 + - - +
247A PHE* 3.4 31.8 - - + +
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Residues in contact with ALA 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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160A THR 2.8 16.2 + - - +
161A TRP 3.6 4.0 - - - +
163A GLN* 1.3 77.3 - - - +
165A ALA* 1.3 52.7 + - - +
167A ALA 3.4 0.2 + - - -
168A ALA* 2.7 39.9 + - - +
175A ALA* 3.8 10.5 - - - +
178A LEU* 3.7 6.5 - - + +
179A VAL* 3.6 26.7 - - + -
247A PHE* 3.6 24.1 - - + -
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Residues in contact with ALA 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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161A TRP* 2.8 29.3 + - + +
162A PRO* 3.7 8.3 - - + +
163A GLN 3.3 0.2 - - - -
164A ALA* 1.3 76.8 - - - +
166A LYS* 1.3 61.7 + - - +
168A ALA* 4.1 0.2 - - - +
169A GLN* 2.9 47.2 + - - +
175A ALA* 3.7 20.6 - - + +
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Residues in contact with LYS 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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162A PRO* 3.0 19.3 + - - +
163A GLN* 3.1 37.5 + - - +
164A ALA 3.3 0.2 - - - -
165A ALA* 1.3 78.1 - - - +
167A ALA* 1.3 62.1 + - - +
169A GLN* 3.6 8.8 + - - +
170A SER* 3.3 19.2 + - - -
244A GLU* 4.8 14.0 + - - -
248A GLN* 6.0 4.7 - - - +
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Residues in contact with ALA 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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163A GLN 3.0 17.6 + - - +
166A LYS* 1.3 75.2 - - - +
168A ALA* 1.3 62.8 + - - +
170A SER* 2.7 25.6 + - - -
171A LEU* 3.1 11.8 + - - +
178A LEU* 3.6 20.6 - - + -
247A PHE* 4.1 25.4 - - + +
250A TYR* 4.7 3.4 - - + -
251A ALA* 4.1 11.2 - - + -
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Residues in contact with ALA 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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164A ALA 2.7 22.6 + - - +
165A ALA 4.1 1.1 - - - +
167A ALA* 1.3 73.5 - - - +
169A GLN* 1.3 51.7 + - + +
171A LEU* 3.0 1.8 + - - -
172A GLY 2.7 30.8 + - - -
173A VAL* 3.0 41.0 + - + +
174A PRO 3.7 4.3 - - - +
175A ALA* 3.6 21.3 - - + +
178A LEU* 3.7 9.4 - - + +
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Residues in contact with GLN 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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165A ALA* 2.9 40.5 + - - +
166A LYS* 3.9 6.9 - - - +
168A ALA* 1.3 77.2 - - + +
170A SER* 1.3 60.4 + - - +
172A GLY* 3.3 12.8 + - - +
173A VAL 4.7 2.7 - - - +
175A ALA* 6.1 0.9 - - + +
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Residues in contact with SER 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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166A LYS 3.3 10.0 + - - -
167A ALA* 2.7 22.6 + - - -
169A GLN* 1.3 77.4 - - - +
171A LEU* 1.3 65.0 + - - +
172A GLY 3.4 0.2 - - - -
251A ALA* 4.1 13.0 + - - +
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Residues in contact with LEU 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 ALA 3.1 18.6 + - - +
168A ALA* 3.0 8.1 + - - +
170A SER* 1.3 82.1 - - - +
172A GLY* 1.3 62.3 + - - +
173A VAL* 3.3 11.8 + - + +
178A LEU* 4.5 9.0 - - + -
250A TYR* 3.7 32.8 - - + +
251A ALA* 4.5 5.6 - - - +
254A VAL* 4.0 14.1 - - + +
255A GLY* 3.4 38.6 - - - +
263A VAL* 4.9 8.1 - - + -
264A ALA* 3.1 35.6 - - + +
265A GLY 3.2 1.0 + - - -
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Residues in contact with GLY 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 ALA 2.7 7.3 + - - -
169A GLN* 3.3 12.2 + - - -
170A SER 3.4 0.8 + - - -
171A LEU* 1.3 78.6 - - - +
173A VAL* 1.3 57.0 + - - -
174A PRO* 4.8 0.3 - - - +
265A GLY* 3.4 24.8 - - - +
266A LYS 4.2 0.9 - - - +
267A THR* 4.9 4.7 - - - +
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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