Contacts of the helix formed by residues 148 - 157 (chain D) in PDB entry 7CE1
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 148 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D SER* 5.3 4.1 + - - -
141D ILE* 4.4 8.5 - - - +
143D LYS 5.0 1.4 - - - +
144D ILE* 3.9 10.4 - - + +
145D GLU* 2.6 35.5 - - - +
146D PRO 4.0 1.2 + - - -
147D ASN* 1.3 83.1 + - - +
149D PRO* 1.3 81.6 - - - +
150D ARG* 3.5 5.6 + - - +
151D VAL* 2.5 44.1 + - + +
152D ARG* 3.1 19.8 + - - +
167D SER* 5.0 0.4 - - - +
171D ILE* 5.8 2.5 - - - +
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Residues in contact with PRO 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D SER* 5.1 9.6 - - - +
124D MET* 5.8 8.3 - - + -
145D GLU* 5.0 2.0 - - - +
147D ASN 4.6 1.8 - - - +
148D ASP* 1.3 99.6 - - - +
150D ARG* 1.3 58.1 + - + +
152D ARG* 3.2 6.5 + - + +
153D PHE* 2.6 33.8 + - - +
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Residues in contact with ARG 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D SER* 4.9 13.5 - - - +
124D MET* 5.2 6.5 - - + -
127D ILE* 4.2 28.5 - - + -
141D ILE* 5.3 4.9 - - + -
148D ASP* 4.2 6.5 + - - +
149D PRO* 1.3 81.9 - - + +
151D VAL* 1.3 66.6 + - - +
153D PHE* 3.6 12.3 - - + -
154D MET* 3.1 33.1 + - + +
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ILE* 4.5 8.5 - - + -
144D ILE* 4.1 10.5 - - + -
148D ASP* 2.5 56.8 - - + +
149D PRO 3.0 0.2 - - - -
150D ARG* 1.3 79.8 - - - +
152D ARG* 1.3 54.9 + - - +
154D MET* 4.9 1.6 - - - -
155D THR* 2.5 31.9 + - - +
161D PHE* 3.8 13.3 - - + -
163D THR* 5.0 0.4 - - + -
167D SER* 5.0 2.0 - - - +
171D ILE* 4.4 15.9 - - + -
173D HIS* 3.3 37.2 - - + +
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Residues in contact with ARG 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ASN* 5.4 4.7 - - - +
148D ASP 3.1 8.7 + - - +
149D PRO* 3.6 7.0 - - + +
151D VAL* 1.3 79.3 - - - +
153D PHE* 1.3 66.4 + - - +
155D THR* 3.0 8.8 + - - -
156D GLU* 2.9 41.2 + - + +
171D ILE* 5.5 9.6 - - + -
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Residues in contact with PHE 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D MET* 5.4 7.0 - - + -
127D ILE* 3.7 28.7 - - + -
128D ARG* 4.1 23.1 - - + -
131D LEU* 4.4 8.5 - - + -
132D GLU* 6.5 0.9 - - + -
149D PRO 2.6 21.6 + - - +
150D ARG* 3.3 12.3 + - + +
152D ARG* 1.3 74.3 - - - +
154D MET* 1.3 60.9 + - - +
156D GLU* 3.4 15.2 + - + +
157D ARG* 3.3 49.6 + - - -
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Residues in contact with MET 154 (chain D).
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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127D ILE* 3.6 40.2 - - + -
131D LEU* 3.9 11.4 - - + -
139D VAL* 4.0 25.6 - - - -
141D ILE* 4.2 22.4 - - + -
150D ARG* 3.1 18.6 + - + +
153D PHE* 1.3 72.9 - - - +
155D THR* 1.3 62.5 + - - +
157D ARG 3.7 0.3 + - - -
158D LYS 3.3 2.3 + - - -
159D MET* 2.8 52.7 + - + +
161D PHE* 3.4 38.1 - - + -
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Residues in contact with THR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D VAL* 2.5 22.7 + - - +
152D ARG* 3.0 11.1 + - - -
154D MET* 1.3 79.8 - - - +
156D GLU* 1.3 62.6 + - + +
158D LYS* 3.4 11.7 + - - +
159D MET 5.0 0.7 - - - +
161D PHE* 3.3 22.0 - - + -
171D ILE* 5.1 18.3 - - + +
172D GLU 5.7 4.5 - - - +
173D HIS* 5.2 3.3 - - + +
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Residues in contact with GLU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ARG* 2.9 32.8 + - + +
153D PHE* 3.4 8.1 + - + +
154D MET 3.3 0.2 - - - -
155D THR* 1.3 80.3 - - + +
157D ARG* 1.3 62.7 + - + +
158D LYS* 3.2 2.5 + - - +
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Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LEU* 3.6 41.5 + - + +
132D GLU* 5.9 5.2 - - - +
153D PHE* 3.3 46.9 + - - +
154D MET 3.7 0.4 + - - +
155D THR 3.4 0.2 - - - -
156D GLU* 1.3 77.9 - - + +
158D LYS* 1.3 71.0 + - - +
159D MET* 3.1 4.8 + - - +
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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