Contacts of the helix formed by residues 151 - 164 (chain A) in PDB entry 1D0K
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A TRP* 3.4 18.8 - - + -
149A GLY 3.7 3.4 - - - +
150A VAL* 1.3 89.4 - - + +
152A PRO* 1.3 77.0 - - + +
153A GLU* 3.6 17.0 - - + +
154A ILE* 3.0 32.3 + - + +
155A ILE* 3.4 10.9 + - - +
265A TRP* 3.5 27.4 - - + +
268A GLY 6.0 0.4 - - - +
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Residues in contact with PRO 152 (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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134A TRP* 3.4 32.8 - - + +
141A LEU* 4.1 39.7 - - + +
142A ASN* 4.4 10.5 - - - +
145A TRP* 4.4 12.1 - - + -
150A VAL 4.3 2.0 - - - +
151A PRO* 1.3 86.7 - - + +
153A GLU* 1.3 63.2 + - - +
155A ILE* 3.3 2.7 + - + +
156A VAL* 2.8 37.1 + - - +
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Residues in contact with GLU 153 (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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134A TRP* 3.8 21.6 - - + -
151A PRO* 3.6 24.0 - - + +
152A PRO* 1.3 82.1 - - - +
154A ILE* 1.3 64.6 + - + +
156A VAL* 4.4 0.9 - - - -
157A GLY* 2.9 22.2 + - - -
348A VAL 4.4 0.7 - - - +
349A TRP* 5.6 3.1 - - + +
352A GLY* 3.2 39.4 - - - +
353A GLN* 4.4 6.9 - - + +
356A ALA* 3.8 15.8 - - + +
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Residues in contact with ILE 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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150A VAL* 3.9 14.8 - - + -
151A PRO* 3.0 29.3 + - + +
153A GLU* 1.3 78.8 - - + +
155A ILE* 1.3 61.8 + - - +
157A GLY* 3.2 1.6 + - - -
158A ILE* 3.0 29.5 + - + +
260A PHE* 3.6 36.1 - - + -
265A TRP* 3.6 23.3 - - + -
271A VAL* 4.7 0.7 - - + -
335A ILE* 4.2 14.1 - - + -
348A VAL* 4.0 5.0 - - + +
349A TRP* 4.1 31.6 - - + -
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Residues in contact with ILE 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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133A PHE* 5.8 0.2 - - + -
141A LEU* 3.9 24.2 - - + +
144A ALA* 3.8 29.6 - - + -
150A VAL* 4.0 25.6 - - + +
151A PRO 3.4 9.3 + - - +
152A PRO* 3.3 2.5 + - + +
154A ILE* 1.3 75.5 - - - +
156A VAL* 1.3 62.1 + - - +
158A ILE* 3.3 1.4 + - - +
159A ILE* 3.1 36.0 + - + +
253A ILE* 3.9 27.8 - - + +
256A VAL* 4.3 20.6 - - + -
257A ALA* 3.8 16.4 - - + -
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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
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130A GLY 4.0 15.9 - - - +
133A PHE* 4.3 10.1 - - + -
134A TRP* 3.8 18.6 - - + -
141A LEU* 3.8 29.8 - - + -
152A PRO 2.8 29.3 + - - +
153A GLU* 4.1 3.8 - - - +
155A ILE* 1.3 71.4 - - - +
157A GLY* 1.3 57.2 + - - +
159A ILE* 5.0 0.2 - - - -
160A GLY* 3.0 12.0 + - - -
165A TRP* 2.9 46.4 + - + +
352A GLY* 5.4 0.9 - - - -
355A VAL* 4.1 18.6 - - + -
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A GLU 2.9 15.2 + - - -
154A ILE 3.2 1.3 + - - -
156A VAL* 1.3 79.6 - - - +
158A ILE* 1.3 55.4 + - - +
160A GLY* 3.3 0.3 + - - -
161A VAL* 2.9 36.0 + - - +
348A VAL* 3.5 28.0 - - - -
351A LEU* 3.9 7.0 - - - +
352A GLY* 4.2 7.6 - - - -
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Residues in contact with ILE 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 ILE 3.0 20.6 + - - +
155A ILE 3.3 4.2 + - - +
157A GLY* 1.3 74.9 - - - +
159A ILE* 1.3 60.0 + - + +
161A VAL* 3.3 0.9 + - - +
162A GLU* 2.9 36.6 + - + +
224A GLY* 5.1 0.4 - - - +
256A VAL* 4.0 15.9 - - + -
260A PHE* 3.8 33.2 - - + -
335A ILE* 4.5 1.6 - - + -
338A TYR* 3.7 40.2 - - + +
344A TYR* 3.4 22.4 - - + +
348A VAL* 3.7 21.5 - - + +
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Residues in contact with ILE 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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133A PHE* 4.0 19.5 - - + -
155A ILE* 3.1 23.3 + - + +
158A ILE* 1.3 76.4 - - + +
160A GLY* 1.3 57.5 + - - +
163A THR* 3.1 22.6 + - - +
165A TRP* 3.2 38.1 + - + -
223A TYR* 3.7 37.0 - - + +
249A PRO 5.0 0.2 - - - +
252A ALA* 4.5 12.8 - - + +
253A ILE* 4.0 26.7 - - + +
256A VAL* 4.4 13.2 - - + -
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Residues in contact with GLY 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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121A PHE* 5.0 0.3 - - - -
126A ASN* 4.7 3.3 + - - -
156A VAL 3.0 11.9 + - - -
157A GLY 3.7 1.1 - - - -
159A ILE* 1.3 76.2 - - - +
161A VAL* 1.3 61.0 + - - +
164A ARG* 2.9 30.9 + - - +
165A TRP* 3.2 37.0 - - - +
351A LEU* 4.1 5.8 - - - -
1C AMU 3.9 0.3 + - - -
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Residues in contact with VAL 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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117A TYR* 5.0 0.4 - - - +
121A PHE* 3.7 37.6 - - + -
157A GLY 2.9 18.8 + - - +
158A ILE 4.1 0.9 - - - +
160A GLY* 1.3 75.3 - - - +
162A GLU* 1.3 56.8 + - - +
344A TYR* 3.6 33.2 - - + +
347A ALA* 4.2 4.7 - - + +
348A VAL* 3.8 27.6 - - + +
351A LEU* 3.9 14.4 - - + -
1C AMU 2.8 21.3 + - - -
2C NAG 3.5 15.4 - - - +
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Residues in contact with GLU 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 ILE* 2.9 26.5 + - + +
159A ILE 4.2 0.2 - - - +
161A VAL* 1.3 77.8 - - - +
163A THR* 1.3 63.9 + - - +
223A TYR 3.9 15.5 - - - +
224A GLY 3.8 11.4 - - - +
225A GLN* 3.3 18.1 - - + +
338A TYR* 3.6 7.4 - - + -
344A TYR* 2.7 32.2 + - - +
1B AMU 2.9 24.9 + - - +
1C AMU 3.5 2.4 - - - -
2C NAG 2.7 59.6 + - - +
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Residues in contact with THR 163 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.1 7.7 + - - +
162A GLU* 1.3 83.1 - - - +
164A ARG* 1.3 68.2 + - - +
165A TRP* 3.9 0.5 - - - -
166A GLY 3.0 18.8 + - - -
167A ARG 3.0 3.3 + - - -
168A VAL* 2.9 46.3 + - - +
169A MET* 3.9 6.5 - - + -
222A GLY 3.3 18.2 - - - +
223A TYR* 2.9 26.9 + - - +
225A GLN* 3.6 13.9 - - + +
1C AMU 4.2 1.6 - - - -
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Residues in contact with ARG 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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121A PHE* 6.1 0.7 - - + -
125A ASP* 4.2 17.0 + - - -
126A ASN* 3.6 26.1 + - - +
129A ASN* 4.6 3.2 - - - +
160A GLY 2.9 19.1 + - - +
162A GLU 3.9 0.2 - - - -
163A THR* 1.3 78.2 - - - +
165A TRP* 1.3 77.3 + - + +
167A ARG* 3.0 53.1 + - + +
168A VAL* 3.7 24.6 - - + +
1C AMU 3.7 26.1 + - - +
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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