Contacts of the helix formed by residues 131 - 141 (chain A) in PDB entry 1EE8
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 ALA 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A PRO* 5.1 1.2 - - - +
128A GLU 4.8 4.5 - - - +
129A ALA 3.0 10.9 + - - +
130A PHE* 1.3 76.7 - - - +
132A PHE* 1.3 64.7 + - - +
133A PRO* 3.5 12.7 - - + -
134A GLY* 3.6 5.6 + - - +
135A PHE* 3.1 21.7 + - - +
191A TYR* 3.8 5.4 - - - -
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Residues in contact with PHE 132 (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 ALA* 1.3 69.4 - - - +
133A PRO* 1.3 70.6 - - + +
135A PHE* 4.1 5.4 - + - -
136A PHE* 2.6 55.5 + + + +
184A GLU* 3.6 36.3 - - + -
187A ALA* 3.4 16.2 - - + -
188A ARG* 3.2 60.8 - - + -
191A TYR* 3.7 41.3 + + + -
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Residues in contact with PRO 133 (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 ALA* 3.5 12.8 - - + -
132A PHE* 1.3 99.8 - - + +
134A GLY* 1.3 58.0 + - - +
136A PHE* 3.7 4.5 - - + +
137A ARG* 2.8 43.0 + - - +
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Residues in contact with GLY 134 (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 ALA* 3.6 7.6 + - - +
132A PHE 3.3 0.4 - - - -
133A PRO* 1.3 77.9 - - - +
135A PHE* 1.3 52.9 + - - +
137A ARG* 3.3 24.6 + - - +
138A GLY* 2.7 33.4 + - - -
155A LEU* 5.9 0.2 - - - +
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Residues in contact with PHE 135 (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 PHE* 3.8 32.5 - + + -
131A ALA 3.1 18.2 + - - +
132A PHE* 3.5 10.3 - + - +
134A GLY* 1.3 75.5 - - - +
136A PHE* 1.3 65.6 + - - +
138A GLY* 3.1 3.9 + - - -
139A LEU* 3.1 60.1 + - + +
149A LEU 6.2 0.2 - - - -
150A LEU* 4.4 13.7 - - + -
155A LEU* 4.6 20.9 - - + +
156A ALA* 5.3 2.2 - - + -
187A ALA 3.7 19.1 - - - -
190A LEU* 4.1 21.1 - - + -
191A TYR* 4.0 26.5 - + + -
194A LEU* 4.6 5.4 - - + -
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Residues in contact with PHE 136 (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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132A PHE* 2.6 36.5 + + + +
133A PRO* 3.7 4.7 - - + +
135A PHE* 1.3 75.7 - - - +
137A ARG* 1.3 64.6 + - - +
139A LEU* 2.9 22.3 + - + +
140A LYS* 3.0 48.4 + - + +
182A LEU* 4.3 2.9 - - + -
183A THR 4.0 1.8 - - - -
184A GLU* 3.3 55.4 - - + -
187A ALA* 3.4 22.0 - - + -
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Residues in contact with ARG 137 (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 PRO* 2.8 30.2 + - - +
134A GLY* 3.5 21.5 + - - +
136A PHE* 1.3 74.1 - - - +
138A GLY* 1.3 63.7 + - - +
139A LEU 3.2 0.5 + - - -
140A LYS* 3.2 15.3 + - - +
141A GLU* 3.3 38.0 + - + +
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Residues in contact with GLY 138 (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 GLY 2.7 18.7 + - - -
135A PHE 3.1 5.3 + - - -
137A ARG* 1.3 74.5 - - - +
139A LEU* 1.3 59.5 + - - +
141A GLU* 3.8 12.8 + - - +
142A SER* 3.4 17.0 + - - -
149A LEU* 3.5 4.3 - - - +
155A LEU* 3.7 24.3 - - - +
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Residues in contact with LEU 139 (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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135A PHE* 3.2 52.0 - - + +
136A PHE* 2.9 10.8 + - + +
138A GLY* 1.3 75.8 - - - +
140A LYS* 1.3 62.2 + - + +
141A GLU 3.1 6.0 + - - -
142A SER 3.2 10.9 + - - +
146A LEU* 4.1 17.0 - - + -
149A LEU* 3.6 24.2 - - + -
150A LEU* 5.3 2.2 - - + -
155A LEU* 4.0 11.4 - - + -
179A ALA* 3.5 14.5 - - - +
180A ARG 3.3 16.5 + - - -
182A LEU* 4.3 14.8 - - + -
187A ALA* 4.2 18.6 - - + -
190A LEU* 4.9 0.2 - - + -
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Residues in contact with LYS 140 (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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136A PHE* 3.0 47.6 + - + +
137A ARG* 3.2 9.2 + - + +
139A LEU* 1.3 76.9 - - + +
141A GLU* 1.3 60.2 + - + +
142A SER 3.3 0.4 - - - -
179A ALA 5.5 0.2 - - - +
180A ARG* 2.6 52.5 + - + +
181A SER 4.5 1.0 + - - -
182A LEU* 2.9 22.9 + - - -
183A THR* 4.9 1.9 - - - +
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Residues in contact with GLU 141 (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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137A ARG* 3.3 38.6 + - + +
138A GLY* 4.2 10.4 - - - +
139A LEU 3.1 1.4 - - - -
140A LYS* 1.3 79.8 - - + +
142A SER* 1.3 61.9 + - - +
143A ALA 4.3 0.2 + - - -
180A ARG* 4.0 11.8 + - - +
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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