Contacts of the helix formed by residues 154 - 166 (chain A) in PDB entry 1E1K
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 GLY 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLY 3.5 4.0 + - - -
153A GLN* 1.3 79.2 - - - +
155A ASN* 1.3 66.0 + - - -
156A VAL 3.2 3.1 - - - -
157A ALA* 3.1 13.2 + - - +
158A LEU* 3.3 13.2 + - - +
204A ALA* 4.0 9.2 - - - -
205A PHE* 3.8 6.1 - - - -
328A SER 5.1 0.4 + - - -
802A NAP 3.6 27.1 + - - -
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Residues in contact with ASN 155 (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 GLY* 1.3 69.7 - - - -
156A VAL* 1.3 67.4 + - - +
158A LEU* 3.2 5.4 + - - +
159A ASP* 2.9 25.6 + - - +
204A ALA 4.4 2.0 + - - -
205A PHE* 3.1 11.7 - - - +
206A THR* 3.0 47.9 + - - +
209A GLU* 3.5 20.4 - - + +
375A VAL* 5.4 0.2 - - - +
802A NAP 3.4 63.0 + - + +
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA* 3.8 17.5 - - + -
127A VAL* 4.5 7.4 - - + -
154A GLY 3.2 0.6 - - - -
155A ASN* 1.3 79.1 - - - +
157A ALA* 1.3 63.1 + - - +
159A ASP* 3.2 8.9 + - + +
160A VAL* 3.0 22.0 + - - +
328A SER* 3.3 15.3 - - - +
331A TYR* 4.3 9.4 - - - +
801A FAD 3.7 44.2 - - + -
802A NAP 3.3 38.1 + - + +
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Residues in contact with ALA 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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150A ILE* 3.6 26.0 - - + +
152A GLY 3.2 27.1 - - - +
154A GLY 3.1 15.5 + - - +
156A VAL* 1.3 79.7 - - - +
158A LEU* 1.4 58.6 + - + +
160A VAL* 3.3 2.7 + - - -
161A ALA* 2.9 29.9 + - - +
194A ILE* 4.0 9.2 - - + -
328A SER* 3.4 11.9 + - - +
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Residues in contact with LEU 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 GLY 3.3 10.5 + - - +
155A ASN* 3.2 8.4 + - - +
157A ALA* 1.4 78.5 - - - +
159A ASP* 1.3 62.6 + - - +
161A ALA* 3.8 2.5 - - - +
162A ARG* 2.8 30.5 + - - +
194A ILE* 3.5 26.0 - - + -
205A PHE* 3.5 43.7 - - + -
209A GLU* 3.7 19.5 - - + +
210A LEU* 3.7 30.3 - - + +
213A MET* 4.1 18.5 - - + +
272A TRP* 5.3 2.7 - - + -
274A LEU* 5.2 2.2 - - + -
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Residues in contact with ASP 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLY 4.4 1.6 - - - +
52A ALA* 4.0 14.3 + - + +
55A HIS* 3.4 10.8 + - - -
127A VAL* 5.4 2.6 - - + +
130A TYR* 3.8 13.6 + - - +
155A ASN 2.9 18.0 + - - +
156A VAL* 3.2 9.3 + - - +
158A LEU* 1.3 76.2 - - - +
160A VAL* 1.3 65.9 + - + +
162A ARG* 3.0 34.1 + - - +
163A ILE* 2.9 29.1 + - - +
209A GLU* 4.9 2.6 - - - +
801A FAD 3.8 26.3 + - - +
802A NAP 4.1 6.5 - - - -
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Residues in contact with VAL 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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123A ALA* 4.1 17.3 - - + +
126A PHE* 3.7 21.5 - - + -
127A VAL* 3.7 30.1 - - + -
130A TYR* 4.2 4.5 - - - +
150A ILE* 4.0 6.7 - - + -
156A VAL 3.0 12.9 + - - +
157A ALA* 3.9 3.6 - - - +
159A ASP* 1.3 78.9 - - - +
161A ALA* 1.3 62.8 + - - +
163A ILE* 3.4 3.4 + - - +
164A LEU* 3.0 26.5 + - + +
326A LEU* 3.0 35.0 - - + -
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Residues in contact with ALA 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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150A ILE* 3.6 16.5 - - + +
157A ALA 2.9 16.7 + - - +
158A LEU 3.8 2.7 - - - +
160A VAL* 1.3 76.9 - - - +
162A ARG* 1.3 63.3 + - - +
164A LEU* 3.2 3.1 + - - +
165A LEU* 2.9 29.5 + - - +
192A VAL* 3.7 17.7 - - + -
194A ILE* 3.8 17.5 - - + -
213A MET* 3.8 14.1 - - + -
272A TRP* 5.5 0.4 - - + -
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Residues in contact with ARG 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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52A ALA* 3.3 10.1 - - - +
54A ASP* 2.7 39.0 + - - +
55A HIS* 3.2 17.5 - - - -
158A LEU* 2.8 25.6 + - - +
159A ASP* 3.0 40.5 + - - +
161A ALA* 1.3 77.3 - - - +
163A ILE* 1.4 55.5 + - - +
165A LEU 3.2 0.7 + - - -
166A THR* 2.6 48.5 + - - +
209A GLU* 4.8 5.9 + - - +
212A GLU* 3.5 37.8 + - - +
213A MET* 3.8 17.4 - - - -
216A LEU* 4.0 18.6 - - + +
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Residues in contact with ILE 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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52A ALA* 4.9 0.2 - - + -
53A PRO* 4.2 20.4 - - + -
54A ASP* 3.8 32.5 - - - +
126A PHE* 4.9 3.4 - - + -
129A TRP* 6.1 0.2 - - + -
130A TYR* 3.7 39.5 - - + +
159A ASP 2.9 21.2 + - - +
160A VAL 3.9 3.6 - - - +
162A ARG* 1.4 78.6 - - - +
164A LEU* 1.3 63.4 + - - +
165A LEU 3.3 0.2 + - - -
166A THR* 3.8 8.4 + - - +
171A LEU* 4.3 18.2 - - + +
176A ILE* 4.4 4.3 - - + -
184A LEU* 3.7 36.3 - - + +
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Residues in contact with LEU 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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126A PHE* 3.8 24.0 - - + -
143A LEU* 4.2 19.5 - - + -
148A ALA* 4.0 26.2 - - + -
150A ILE* 4.8 2.2 - - + -
160A VAL* 3.0 34.9 + - + +
161A ALA* 3.2 6.0 + - - +
163A ILE* 1.3 78.1 - - - +
165A LEU* 1.3 62.6 + - + +
184A LEU* 4.4 14.4 - - + +
187A SER* 5.0 3.5 + - - +
189A VAL* 4.5 17.1 - - + +
192A VAL* 4.2 15.3 - - + -
270A ARG* 3.2 17.0 + - - -
324A LEU* 4.2 4.5 - - + -
326A LEU* 4.2 8.7 - - + -
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Residues in contact with LEU 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 ALA 2.9 16.8 + - - +
164A LEU* 1.3 84.0 - - - +
166A THR* 1.3 65.6 + - - +
167A PRO* 3.4 4.3 - - - +
189A VAL* 4.2 11.9 - - + +
190A LYS 4.2 7.6 - - - -
192A VAL* 3.7 24.9 - - + -
213A MET* 4.2 6.1 - - + -
216A LEU* 4.0 14.1 - - + -
217A PRO 4.7 0.2 - - - +
218A GLY 5.8 0.2 - - - -
219A THR* 4.0 15.6 - - + +
270A ARG* 3.5 36.3 - - + +
271A ALA 3.4 27.8 - - - +
272A TRP* 3.6 22.2 - - + -
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Residues in contact with THR 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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54A ASP* 4.4 5.2 + - - +
162A ARG* 2.6 36.3 + - - +
163A ILE* 3.8 3.9 + - - +
164A LEU 3.7 1.2 - - - -
165A LEU* 1.3 73.2 - - - +
167A PRO* 1.3 88.3 - - + +
168A PRO* 3.0 9.7 - - - +
170A HIS* 3.7 16.4 - - + +
171A LEU* 3.8 28.4 - - + +
216A LEU* 3.4 23.5 - - + +
270A ARG* 3.9 5.1 + - - -
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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