Contacts of the helix formed by residues 161 - 174 (chain A) in PDB entry 1CK4
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 PRO 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A TYR* 1.3 102.6 - - + +
162A TRP* 1.3 65.2 + - - +
163A GLU* 3.2 9.6 - - + +
164A SER* 2.8 34.3 + - - +
165A VAL* 3.6 5.9 + - - +
291A ARG* 4.8 2.2 - - - +
321A GLU* 3.7 29.7 - - + +
322A LEU* 5.4 8.1 - - + +
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Residues in contact with TRP 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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153A LEU* 3.5 36.8 - - + -
154A ASP 4.1 14.1 - - - -
159A ILE* 4.2 8.1 - - + -
160A TYR 2.2 16.4 + - - -
161A PRO* 1.3 67.3 - - - +
163A GLU* 1.3 61.2 + - - +
164A SER 2.8 6.2 + - - -
165A VAL* 2.8 38.0 + - + +
166A ILE* 3.2 28.5 + - + +
189A GLN* 3.6 20.6 - - - -
216A ILE* 3.0 25.3 + - + -
217A GLY* 4.2 2.9 - - - -
218A ARG* 3.0 68.7 - - + +
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PRO* 4.7 7.2 - - + +
162A TRP* 1.3 78.5 - - - +
164A SER* 1.3 57.3 + - - +
165A VAL 3.4 0.2 - - - -
166A ILE* 3.6 14.0 - - + +
167A ALA* 2.8 32.9 + - - +
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PRO* 2.8 32.9 + - - +
162A TRP 2.8 0.4 + - - -
163A GLU* 1.3 82.6 + - - +
165A VAL* 1.3 62.7 + - - +
167A ALA* 3.5 8.0 + - - +
168A PHE* 3.2 20.3 + - - +
321A GLU* 4.1 23.4 - - - +
322A LEU* 3.9 18.7 - - - +
324A LEU* 3.9 6.8 - - - +
325A VAL* 5.4 3.3 - - - +
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Residues in contact with VAL 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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153A LEU* 3.4 35.0 - - + -
159A ILE* 3.2 35.4 - - + -
161A PRO 3.9 3.8 - - - +
162A TRP* 2.8 29.1 + - + +
164A SER* 1.3 76.4 - - - +
166A ILE* 1.3 59.5 + - + +
168A PHE* 3.1 9.7 + - + +
169A LEU* 2.8 32.5 + - + +
255A VAL* 4.5 13.5 - - + -
285A ILE* 5.3 0.4 - - + -
321A GLU* 5.5 0.4 - - + -
324A LEU* 4.1 15.0 - - + -
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Residues in contact with ILE 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 TRP* 3.4 32.1 - - + +
163A GLU* 3.6 13.5 - - + +
165A VAL* 1.3 74.9 - - - +
167A ALA* 1.3 60.1 + - - +
169A LEU* 3.2 13.1 + - + +
170A ASN* 2.8 29.1 + - - +
213A ALA 4.3 6.5 - - - +
214A ASN* 3.2 51.4 - - - +
216A ILE* 3.1 28.9 - - + +
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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 GLU 2.8 21.6 + - - +
164A SER* 3.7 10.1 - - - +
166A ILE* 1.3 75.6 - - - +
168A PHE* 1.3 58.1 + - - +
170A ASN* 3.6 7.4 + - - +
171A ASP* 2.9 29.1 + - - +
214A ASN* 5.8 0.4 - - - +
325A VAL* 3.8 15.7 - - + +
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Residues in contact with PHE 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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151A ILE* 6.0 0.4 - - + -
164A SER 3.2 11.2 + - - +
165A VAL* 3.1 16.3 + - + +
167A ALA* 1.3 76.8 - - - +
169A LEU* 1.3 88.9 + - + +
171A ASP* 2.9 8.9 + - - +
172A LEU* 2.8 41.7 + - + +
253A VAL* 5.3 1.1 - - + -
255A VAL* 4.0 21.3 - - + -
283A ILE* 3.5 24.5 - - + -
324A LEU* 3.7 43.5 - - + -
325A VAL* 4.1 5.5 - - + +
327A ILE* 3.9 22.9 - - + -
328A VAL* 3.9 13.0 - - + -
331A LEU* 4.1 4.7 - - + -
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Residues in contact with LEU 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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151A ILE* 4.0 29.6 - - + -
153A LEU* 4.2 25.1 - - + -
165A VAL* 2.8 20.0 + - + +
166A ILE* 3.5 15.3 - - + +
168A PHE* 1.3 93.9 - - + +
170A ASN* 1.3 62.8 + - - +
172A LEU* 3.1 4.7 + - + +
173A LEU* 2.9 39.4 + - + +
187A ILE* 4.2 22.0 - - + -
213A ALA* 4.6 15.0 - - + +
216A ILE* 4.5 10.8 - - + -
255A VAL* 5.6 0.7 - - + -
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Residues in contact with ASN 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 ILE 2.8 20.0 + - - +
167A ALA* 3.6 8.5 - - - +
169A LEU* 1.3 72.5 - - - +
171A ASP* 1.3 52.4 + - - +
173A LEU* 4.7 0.2 - - - -
174A LYS* 2.7 68.4 + - - +
210A LEU* 3.9 25.0 - - - +
213A ALA* 5.8 3.3 - - - +
214A ASN* 3.0 31.0 + - - +
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Residues in contact with ASP 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 2.9 18.4 + - - +
168A PHE 2.9 7.6 + - - +
170A ASN* 1.3 78.3 - - - +
172A LEU* 1.3 55.8 + - - +
174A LYS* 3.0 29.1 + - - +
175A ARG* 3.3 28.1 + - - -
325A VAL* 3.9 19.7 - - + +
328A VAL* 2.8 41.9 - - + +
329A LYS* 5.0 0.9 - - - -
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Residues in contact with LEU 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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151A ILE* 5.9 4.9 - - + -
168A PHE* 2.8 30.2 + - + +
169A LEU* 3.7 7.6 - - + +
171A ASP* 1.3 75.9 - - - +
173A LEU* 1.3 72.1 + - + +
175A ARG* 3.7 10.1 + - + +
176A MET* 3.4 36.1 - - + +
253A VAL* 4.7 12.1 - - + -
328A VAL* 4.1 11.9 - - + +
331A LEU* 3.3 34.1 - - + -
332A GLY* 4.3 24.9 - - - +
335A ILE* 5.4 1.1 - - + -
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Residues in contact with LEU 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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151A ILE* 5.1 11.4 - - + -
169A LEU* 2.9 28.7 + - + +
172A LEU* 1.3 89.9 - - + +
174A LYS* 1.3 54.2 + - - +
175A ARG 2.7 16.4 + - - -
176A MET* 2.8 31.7 + - + +
178A ILE* 4.3 4.6 - - + +
185A VAL* 3.6 32.5 - - + -
187A ILE* 5.8 1.8 - - + -
198A PHE* 5.4 1.1 - - + -
206A THR* 4.0 5.1 + - - +
209A VAL* 3.5 29.4 - - + -
210A LEU* 3.4 19.5 - - + -
213A ALA* 5.1 9.2 - - + -
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Residues in contact with LYS 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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170A ASN* 2.7 47.2 + - - +
171A ASP* 3.0 40.3 + - - +
173A LEU* 1.3 75.2 - - - +
175A ARG* 1.3 90.2 + - - +
176A MET 4.4 3.1 - - - +
206A THR* 4.4 6.7 - - - +
210A LEU* 3.4 25.9 - - + +
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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