Contacts of the helix formed by residues 148 - 157 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LYS 3.9 0.3 - - - +
144A ILE* 3.9 4.5 - - + -
145A GLU* 3.4 43.8 + - - +
146A PRO 3.7 1.4 - - - -
147A ASN* 1.3 75.1 - - - +
149A PRO* 1.3 68.8 - - - +
150A ARG* 2.9 61.4 + - - +
151A VAL* 3.4 30.6 + - + +
152A ARG* 3.5 4.5 + - - +
169A MET* 3.0 22.2 - - - +
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Residues in contact with PRO 149 (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 SER* 5.2 4.9 - - - +
124A MET* 3.4 25.9 - - + +
145A GLU* 4.3 10.3 - - - +
147A ASN* 3.5 9.4 - - - +
148A ASP* 1.3 89.6 - - - +
150A ARG* 1.3 58.8 + - + +
152A ARG* 3.3 13.2 + - + +
153A PHE* 2.8 29.3 + - - +
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Residues in contact with ARG 150 (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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83A VAL* 4.4 6.5 - - - +
117A HIS* 4.2 19.4 - - - -
123A SER* 3.2 37.8 + - - +
124A MET* 3.4 29.8 - - + -
127A ILE* 3.6 14.1 - - + +
141A ILE* 4.2 20.7 - - + +
142A SER 2.8 29.0 + - - +
143A LYS* 3.1 18.0 + - - +
144A ILE* 4.3 4.2 - - - +
145A GLU* 5.2 1.8 + - - -
148A ASP* 2.9 25.4 + - - +
149A PRO* 1.3 70.7 - - + +
151A VAL* 1.3 64.4 + - - +
153A PHE* 4.2 1.8 - - - -
154A MET* 3.0 45.9 + - + +
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Residues in contact with VAL 151 (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 ILE* 4.3 14.6 - - + -
144A ILE* 4.6 2.5 - - + -
148A ASP* 3.5 32.3 - - + +
149A PRO 3.2 0.2 - - - -
150A ARG* 1.3 78.1 - - - +
152A ARG* 1.3 50.1 + - - +
155A THR* 2.4 37.2 + - - +
161A PHE* 3.8 13.8 - - + -
163A THR* 4.4 9.0 - - + -
167A SER* 3.8 12.8 - - - +
169A MET* 3.5 20.2 - - + -
171A ILE* 4.4 9.0 - - + -
173A HIS* 3.8 25.4 - - + +
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Residues in contact with ARG 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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147A ASN* 3.7 22.4 + - - +
148A ASP 3.5 3.9 + - - +
149A PRO* 3.3 11.7 + - - +
151A VAL* 1.3 77.7 - - - +
153A PHE* 1.3 64.4 + - - +
155A THR* 3.1 6.6 + - - -
156A GLU* 2.9 49.1 + - + +
169A MET* 4.0 22.4 + - - +
171A ILE* 4.1 17.9 - - + +
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Residues in contact with PHE 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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124A MET* 4.1 15.7 - - - -
127A ILE* 3.7 23.1 - - + -
128A ARG* 3.9 36.6 - - + -
131A LEU* 4.5 13.7 - - + -
149A PRO 2.8 18.1 + - - +
150A ARG* 3.8 4.7 - - - +
151A VAL 3.4 0.2 - - - -
152A ARG* 1.3 81.6 - - - +
154A MET* 1.3 57.5 + - - +
156A GLU* 3.7 11.1 - - - +
157A ARG* 2.8 84.5 + - + +
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Residues in contact with MET 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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127A ILE* 3.6 42.2 - - + -
131A LEU* 4.1 10.8 - - + -
139A VAL* 4.0 16.4 - - + -
141A ILE* 3.8 24.2 - - + -
150A ARG* 3.0 32.4 + - + +
153A PHE* 1.3 73.5 - - - +
155A THR* 1.3 62.2 + - - +
157A ARG* 4.4 2.5 - - - +
158A LYS 2.9 6.4 + - - -
159A MET* 2.7 53.2 + - + +
161A PHE* 3.8 29.8 - - + -
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Residues in contact with THR 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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151A VAL 2.4 29.7 + - - +
152A ARG* 3.1 14.9 + - - -
154A MET* 1.3 75.6 - - - +
156A GLU* 1.3 60.0 + - - +
158A LYS* 3.4 12.4 + - - +
159A MET 5.2 0.2 - - - -
161A PHE* 3.4 28.0 - - + -
171A ILE* 3.5 32.9 - - + +
172A GLU 5.2 1.6 - - - +
173A HIS* 5.1 1.6 - - + -
326A ARG* 6.0 4.5 - - - +
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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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152A ARG* 2.9 39.4 + - + +
153A PHE* 3.7 18.5 - - - +
155A THR* 1.3 78.1 + - - +
157A ARG* 1.3 75.8 + - + +
158A LYS* 3.2 2.5 + - - +
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Residues in contact with ARG 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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131A LEU* 4.3 27.1 - - + +
153A PHE* 2.8 66.3 + - + +
154A MET 4.4 0.9 - - - +
156A GLU* 1.3 90.3 + - + +
158A LYS* 1.3 68.0 + - - +
159A MET 3.3 3.1 + - - -
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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