Contacts of the helix formed by residues 155 - 170 (chain A) in PDB entry 4PKO
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 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A THR* 3.4 12.7 + - - +
152A ALA* 4.2 5.2 + - - +
153A ASN 3.5 2.4 - - - +
154A SER* 1.3 81.8 - - - +
156A GLU* 1.3 63.1 + - - +
157A THR* 3.2 7.4 - - - +
158A VAL* 3.4 30.9 + - + +
159A GLY 3.5 6.2 + - - -
392A LYS* 4.1 11.5 - - - -
395A ARG* 2.9 40.7 + - - -
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Residues in contact with GLU 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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149A THR* 3.5 22.8 + - + +
154A SER 4.0 5.4 + - - +
155A ASP* 1.3 71.4 - - - +
157A THR* 1.3 61.4 + - - +
159A GLY* 3.2 1.1 + - - -
160A LYS* 2.9 32.8 + - - +
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Residues in contact with THR 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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155A ASP* 4.1 8.0 - - - +
156A GLU* 1.3 78.7 + - + +
158A VAL* 1.3 70.1 + - - +
160A LYS* 4.0 3.2 - - - +
161A LEU* 3.0 30.3 + - - +
185A ASP* 3.8 19.8 + - - -
392A LYS* 6.2 0.3 - - - -
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Residues in contact with VAL 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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152A ALA* 3.9 22.4 - - + -
155A ASP* 3.6 30.7 - - + +
156A GLU 3.2 0.4 - - - -
157A THR* 1.3 82.7 + - - +
159A GLY* 1.3 61.8 + - - +
161A LEU* 3.9 5.9 - - - +
162A ILE* 3.2 30.6 + - + +
185A ASP* 4.6 10.3 - - - +
392A LYS* 5.2 6.3 - - - -
395A ARG* 5.4 1.6 - - + -
396A VAL* 4.5 29.8 - - + -
399A ALA* 4.1 13.7 - - + -
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Residues in contact with GLY 159 (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 ILE 4.4 0.5 - - - +
145A ALA* 3.3 35.8 - - - -
148A GLY* 4.0 5.4 - - - -
149A THR* 3.4 14.9 - - - +
155A ASP 3.5 4.8 + - - -
156A GLU 3.2 3.6 + - - -
158A VAL* 1.3 77.5 - - - +
160A LYS* 1.3 63.6 + - - +
162A ILE* 3.4 4.6 + - - +
163A ALA 3.0 17.5 + - - -
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Residues in contact with LYS 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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141A SER* 4.1 27.1 + - - -
142A LYS* 4.9 4.2 - - - +
145A ALA* 3.8 16.6 - - + +
156A GLU 2.9 19.5 + - - +
157A THR* 4.3 3.4 - - - +
159A GLY* 1.3 72.0 - - - -
161A LEU* 1.3 57.0 + - - +
163A ALA* 3.3 4.0 + - + +
164A GLU* 2.9 52.2 + - - +
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Residues in contact with LEU 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 THR* 3.0 20.5 + - - +
158A VAL* 3.9 6.1 - - - +
159A GLY 3.2 0.2 - - - -
160A LYS* 1.3 75.2 - - - +
162A ILE* 1.3 59.9 + - + +
164A GLU* 3.3 17.9 + - - +
165A ALA* 3.0 26.2 + - - +
185A ASP* 4.0 29.8 - - + +
186A GLU 4.3 9.4 - - - +
187A LEU* 3.6 42.7 - - + +
379A ILE* 4.4 17.7 - - + -
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Residues in contact with ILE 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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144A ILE* 4.5 1.6 - - + -
148A GLY* 5.0 1.6 - - - -
158A VAL* 3.2 24.3 + - + +
159A GLY* 3.7 4.3 - - - +
161A LEU* 1.3 73.6 - - + +
163A ALA* 1.3 61.3 + - - +
165A ALA* 3.2 6.3 + - + +
166A MET* 2.8 41.8 + - + +
175A ILE* 6.2 0.2 - - + -
379A ILE* 4.2 18.8 - - + -
396A VAL* 4.6 4.9 - - + +
399A ALA* 3.9 38.8 - - + +
400A LEU* 4.0 18.4 - - + +
403A THR* 3.8 30.1 - - + +
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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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141A SER* 3.2 37.4 + - - +
144A ILE* 4.1 12.0 - - + +
145A ALA* 3.8 12.1 - - + +
159A GLY 3.0 13.5 + - - +
160A LYS* 3.5 14.1 - - + +
161A LEU 3.3 0.2 - - - -
162A ILE* 1.3 77.2 - - - +
164A GLU* 1.3 57.9 + - - +
166A MET* 4.3 1.6 - - - +
167A ASP* 2.9 31.8 + - - +
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Residues in contact with GLU 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 LYS* 2.9 37.8 + - + +
161A LEU* 3.4 23.5 - - - +
162A ILE 3.2 0.2 - - - -
163A ALA* 1.3 77.0 - - - +
165A ALA* 1.3 51.3 + - - +
167A ASP* 3.3 4.7 + - - +
168A LYS* 2.6 43.4 + - + +
187A LEU* 3.5 19.6 - - + +
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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 LEU 3.0 13.6 + - - +
162A ILE* 3.2 11.6 + - + +
164A GLU* 1.3 76.3 - - - +
166A MET* 1.3 58.9 + - + +
168A LYS* 4.2 4.3 - - - -
169A VAL* 2.8 38.3 + - - +
175A ILE* 4.3 23.8 - - + -
187A LEU* 4.1 20.8 - - + +
189A VAL* 5.9 0.7 - - - -
377A ALA* 4.4 7.9 - - + -
379A ILE* 4.9 1.3 - - + -
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Residues in contact with MET 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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144A ILE* 4.2 19.1 - - + -
162A ILE* 2.8 29.6 + - + +
163A ALA 4.3 1.8 - - - +
165A ALA* 1.3 72.8 - - + +
167A ASP* 1.3 57.1 + - - +
169A VAL* 4.3 2.0 - - - -
170A GLY* 3.0 38.3 + - - +
171A LYS* 4.4 31.9 + - + +
175A ILE* 4.6 17.5 - - + -
400A LEU* 6.0 0.9 - - - -
403A THR* 3.8 32.1 - - - +
404A ARG* 4.9 12.3 - - + +
407A VAL* 3.5 29.2 - - + -
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Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER* 2.9 24.6 + - - +
144A ILE* 6.1 0.2 - - - +
163A ALA 2.9 21.9 + - - +
164A GLU* 3.6 5.8 - - - +
166A MET* 1.3 78.1 - - - +
168A LYS* 1.3 65.9 + - - +
170A GLY* 4.0 4.0 + - - -
171A LYS* 5.9 2.0 - - - +
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Residues in contact with LYS 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 GLU* 2.6 25.8 + - + +
165A ALA* 3.6 5.4 - - - +
167A ASP* 1.3 79.3 - - - +
169A VAL* 1.3 63.3 + - + +
170A GLY 3.7 0.2 + - - -
187A LEU* 5.9 2.7 - - + -
189A VAL* 4.4 28.3 - - + -
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Residues in contact with VAL 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* 2.8 30.0 + - - +
166A MET* 4.3 1.6 - - - -
168A LYS* 1.3 76.2 - - + +
170A GLY* 1.3 65.1 + - - +
172A GLU* 4.6 0.7 + - - +
173A GLY* 3.5 32.2 + - - -
175A ILE* 4.6 3.8 - - + -
189A VAL* 4.1 21.5 - - + -
374A GLY* 4.3 6.1 - - - -
375A GLY* 3.7 33.3 + - - +
377A ALA* 3.8 28.9 - - + -
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Residues in contact with GLY 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 MET* 3.0 29.7 + - - +
167A ASP 4.0 3.9 + - - -
168A LYS 3.3 4.0 + - - -
169A VAL* 1.3 85.2 - - - +
171A LYS* 1.3 67.2 + - - +
172A GLU* 3.2 3.9 + - - -
173A GLY* 3.4 5.5 + - - +
175A ILE* 5.7 0.5 - - - +
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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