Contacts of the helix formed by residues 131 - 141 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B GLU 4.4 10.5 - - - +
129B ALA 3.1 8.6 + - - +
130B PHE* 1.3 74.7 - - - +
132B PHE* 1.3 67.2 + - - +
133B PRO* 3.3 13.8 - - + -
134B GLY* 3.4 6.5 + - - +
135B PHE* 3.0 19.8 + - - +
191B TYR* 3.7 4.9 - - - -
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Residues in contact with PHE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ALA* 1.3 72.1 - - - +
133B PRO* 1.3 66.2 - - + +
135B PHE* 3.0 8.4 + + - -
136B PHE* 2.7 63.7 + + + +
184B GLU* 3.9 5.8 - - + -
187B ALA* 3.5 19.7 - - + -
188B ARG* 2.9 72.9 - - + +
191B TYR* 3.4 44.2 - + + -
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Residues in contact with PRO 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ALA* 3.4 13.5 - - + -
132B PHE* 1.3 101.3 - - + +
134B GLY* 1.3 61.7 + - - +
136B PHE* 3.3 5.1 + - + +
137B ARG* 3.0 36.5 + - - +
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ALA* 3.4 7.6 + - - +
132B PHE 3.3 0.2 - - - -
133B PRO* 1.3 79.2 - - - +
135B PHE* 1.3 62.5 + - - +
137B ARG* 3.3 21.0 + - - +
138B GLY* 3.0 19.9 + - - -
155B LEU* 5.8 0.5 - - - +
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Residues in contact with PHE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PHE* 3.7 31.4 - + + -
131B ALA 3.0 13.6 + - - +
132B PHE* 3.0 17.2 + + - +
134B GLY* 1.3 76.6 - - - +
136B PHE* 1.3 63.9 + - - +
138B GLY* 3.3 2.6 + - - -
139B LEU* 3.1 47.3 + - + +
150B LEU* 4.3 10.8 - - + -
155B LEU* 3.9 34.6 - - + +
187B ALA 3.7 18.2 - - - -
190B LEU* 3.8 21.8 - - + -
191B TYR* 3.8 28.9 - + + -
194B LEU* 4.6 5.2 - - + -
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE* 2.7 38.2 + + + +
133B PRO* 3.7 5.2 - - + +
135B PHE* 1.3 74.1 - - - +
137B ARG* 1.3 63.4 + - - +
139B LEU* 3.2 8.0 + - + +
140B LYS* 3.1 58.5 + - + +
182B LEU* 3.9 4.7 - - + -
184B GLU* 3.6 37.9 - - + -
187B ALA* 3.5 29.6 - - + -
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PRO* 3.0 18.1 + - - +
134B GLY* 3.5 30.5 - - - +
136B PHE* 1.3 78.1 - - - +
138B GLY* 1.3 63.0 + - - +
140B LYS* 3.3 5.1 + - - +
141B GLU* 3.0 49.7 + - + +
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Residues in contact with GLY 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLY 3.0 14.0 + - - -
135B PHE 3.7 2.9 - - - -
137B ARG* 1.3 77.3 - - - +
139B LEU* 1.3 61.5 + - - +
141B GLU* 3.3 26.0 + - - +
142B SER* 3.6 9.2 + - - -
149B LEU* 4.0 3.8 - - - +
155B LEU* 4.4 19.0 - - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PHE* 3.1 49.0 + - + +
136B PHE* 3.7 7.2 - - - +
138B GLY* 1.3 75.7 - - - +
140B LYS* 1.3 62.4 + - + +
141B GLU 3.0 0.2 - - - -
142B SER 3.0 26.9 + - - +
146B LEU* 3.8 25.1 - - + -
149B LEU* 3.9 11.7 - - + -
150B LEU* 5.2 1.3 - - + -
155B LEU* 3.6 21.3 - - + -
179B ALA* 3.5 13.4 - - + +
180B ARG* 3.1 8.4 + - - -
182B LEU* 4.0 15.7 - - + -
187B ALA* 4.0 21.5 - - + -
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B PHE* 3.1 48.4 + - + +
137B ARG* 3.9 5.2 - - - +
139B LEU* 1.3 80.0 - - + +
141B GLU* 1.3 59.7 + - + +
142B SER 3.1 2.0 + - - -
179B ALA 5.3 0.2 - - - +
180B ARG* 2.6 53.3 + - + +
181B SER 4.5 0.8 - - - -
182B LEU 2.7 25.0 + - - +
183B THR* 4.9 1.5 - - - +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ARG* 3.0 51.1 + - + +
138B GLY* 3.5 13.3 - - - +
139B LEU 3.0 1.0 - - - -
140B LYS* 1.3 76.1 - - + +
142B SER* 1.3 59.6 + - - +
180B ARG* 5.3 2.2 - - - -
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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