Contacts of the helix formed by residues 155 - 167 (chain A) in PDB entry 3EW9
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 ARG 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A HIS* 3.0 17.3 + - + -
152A GLY 3.1 26.6 + - - -
153A THR* 3.3 19.3 - - - +
154A PHE* 1.3 101.5 + - - +
156A PRO* 1.3 70.5 - - - +
157A GLU* 3.1 22.7 - - + +
158A ARG* 3.0 23.4 + - + +
159A VAL* 3.3 13.3 + - - +
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Residues in contact with PRO 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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154A PHE* 3.8 27.7 - - + +
155A ARG* 1.3 85.3 - - - +
157A GLU* 1.3 74.8 + - + +
159A VAL* 3.3 4.0 + - + +
160A VAL* 3.1 29.8 + - - +
174A LEU* 4.2 23.9 - - + +
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Residues in contact with GLU 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 ARG* 3.3 23.8 - - + +
156A PRO* 1.3 94.7 - - + +
158A ARG* 1.3 50.4 + - - +
160A VAL* 3.2 8.3 + - - +
161A GLN* 2.8 35.6 + - - +
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Residues in contact with ARG 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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113A GLN* 2.8 32.3 + - - +
116A HIS* 4.1 11.7 - - + +
155A ARG* 3.0 21.0 + - + +
157A GLU* 1.3 77.5 - - - +
159A VAL* 1.3 60.2 + - - +
161A GLN* 2.6 36.8 + - - +
162A MET* 2.9 55.6 + - + +
315A ILE* 3.7 13.1 - - - +
316A THR 2.8 21.6 + - - -
317A GLU 3.1 20.6 + - - -
319A GLY* 3.6 13.0 - - - +
401A ANP 3.1 27.1 + - - +
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Residues in contact with VAL 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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116A HIS* 3.6 24.9 - - + +
119A CYS* 4.8 4.7 - - + -
120A VAL* 3.4 15.3 - - + +
154A PHE* 3.7 25.4 - - + -
155A ARG 3.4 14.1 - - - +
156A PRO* 3.6 6.5 - - + +
157A GLU 3.2 0.4 - - - -
158A ARG* 1.3 76.6 - - - +
160A VAL* 1.3 59.3 + - - +
162A MET* 4.6 3.4 - - - -
163A ALA* 2.9 26.7 + - - +
170A GLY 5.2 0.2 - - - +
173A VAL* 3.6 33.2 - - + -
174A LEU* 4.2 12.1 - - + -
177A THR* 5.6 1.8 - - + +
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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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156A PRO 3.1 15.8 + - - +
157A GLU* 3.4 11.0 - - - +
159A VAL* 1.3 74.1 - - - +
161A GLN* 1.3 60.2 + - - +
163A ALA* 3.0 4.3 + - - +
164A GLU* 2.9 52.8 + - + +
170A GLY* 4.0 24.0 - - - +
171A GLN* 4.9 0.9 - - - +
174A LEU* 3.9 23.3 - - + -
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Residues in contact with GLN 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 GLU 2.8 20.4 + - - +
158A ARG* 2.6 36.6 + - - +
160A VAL* 1.3 75.5 - - - +
162A MET* 1.3 56.0 + - - +
164A GLU* 3.2 11.8 + - + +
165A GLY* 2.9 25.1 + - - -
317A GLU* 3.5 25.9 + - + +
401A ANP 2.8 18.5 + - - -
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Residues in contact with MET 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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113A GLN* 3.4 31.4 - - + +
116A HIS* 3.7 12.8 - - + +
117A GLN* 3.5 38.3 + - + +
120A VAL* 4.0 9.8 - - + +
158A ARG* 2.9 62.5 + - + +
159A VAL 3.8 4.0 - - - +
161A GLN* 1.3 76.7 - - - +
163A ALA* 1.3 56.8 + - - +
165A GLY 3.4 1.9 + - - -
166A ALA* 2.9 28.2 + - - +
318A LYS 3.2 22.0 - - - +
319A GLY* 3.8 13.5 - - - -
320A ILE 4.6 0.4 - - - +
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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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120A VAL* 3.8 11.4 - - + +
159A VAL 2.9 16.3 + - - +
160A VAL 3.0 10.3 + - - +
162A MET* 1.3 73.0 - - - +
164A GLU* 1.3 55.2 + - - +
166A ALA* 2.9 3.0 + - - +
167A GLY 2.7 30.5 + - - -
168A ILE* 2.9 13.6 + - + +
169A ASP 4.2 1.8 - - - -
170A GLY* 3.5 26.9 - - - +
173A VAL* 4.0 17.0 - - + -
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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 VAL* 2.9 44.2 + - + +
161A GLN* 3.5 13.2 - - + +
163A ALA* 1.3 75.0 - - - +
165A GLY* 1.3 59.8 + - - +
167A GLY* 2.9 19.6 + - - -
168A ILE 3.5 15.2 - - - +
169A ASP* 4.9 0.3 - - - -
170A GLY 4.1 7.6 + - - -
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Residues in contact with GLY 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 GLN 2.9 14.6 + - - -
162A MET 3.6 6.1 - - - -
163A ALA 3.2 0.2 - - - -
164A GLU* 1.3 78.5 - - - +
166A ALA* 1.3 55.7 + - - +
318A LYS* 3.4 51.1 + - - +
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Residues in contact with ALA 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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117A GLN* 5.1 4.3 - - - +
120A VAL* 4.1 5.2 - - + -
124A MET* 3.5 39.8 - - + +
127A LYS* 5.5 2.9 - - - +
162A MET 2.9 15.4 + - - +
163A ALA 2.9 4.9 + - - +
165A GLY* 1.3 76.8 - - - +
167A GLY* 1.3 60.2 + - - +
168A ILE* 4.3 1.5 - - + +
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Residues in contact with GLY 167 (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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163A ALA 2.7 6.7 + - - -
164A GLU* 2.9 13.0 + - - -
166A ALA* 1.3 80.9 - - - +
168A ILE* 1.3 60.1 + - - -
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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