Contacts of the helix formed by residues 141 - 154 (chain A) in PDB entry 2EVT
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 GLY 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A HIS* 1.3 75.3 - - - +
142A TRP* 1.3 62.2 + - - -
143A ILE 3.3 2.7 - - - -
144A VAL 3.5 2.3 + - - -
145A GLN* 3.0 29.1 + - - +
208A LYS* 4.0 12.4 - - - +
209A VAL* 2.8 20.5 + - - -
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Residues in contact with TRP 142 (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 GLY* 1.3 72.4 - - - -
143A ILE* 1.3 100.8 + - + +
145A GLN* 3.4 10.2 + - - +
146A LYS* 3.3 50.4 + - + +
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Residues in contact with ILE 143 (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 GLY 3.3 0.6 - - - -
142A TRP* 1.3 122.0 - - + +
144A VAL* 1.3 67.4 + - + +
146A LYS* 3.4 10.2 + - - +
147A ILE* 3.4 29.8 + - + +
209A VAL 5.9 0.9 - - - +
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Residues in contact with VAL 144 (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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140A HIS* 2.9 39.5 - - + +
141A GLY 3.5 3.2 + - - +
142A TRP 3.4 0.2 - - - -
143A ILE* 1.3 78.5 - - + +
145A GLN* 1.3 66.7 + - - +
147A ILE* 3.1 18.3 + - + +
148A PHE* 3.0 33.3 + - + -
209A VAL* 3.5 44.2 - - + +
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Residues in contact with GLN 145 (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 TYR* 3.4 26.2 + - + +
137A LYS* 3.8 38.1 + - + +
140A HIS* 3.0 24.5 + - + -
141A GLY 3.0 22.5 + - - +
142A TRP* 3.6 9.0 - - - +
143A ILE 3.2 0.2 - - - -
144A VAL* 1.3 77.2 - - - +
146A LYS* 1.3 58.3 + - + +
148A PHE* 3.3 1.6 + - - +
149A GLN* 2.8 33.4 + - - +
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Residues in contact with LYS 146 (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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142A TRP* 3.3 39.6 + - + +
143A ILE* 3.6 8.7 - - - +
144A VAL 3.3 0.4 - - - -
145A GLN* 1.3 75.7 - - + +
147A ILE* 1.3 66.7 + - + +
149A GLN* 3.7 23.5 + - - +
150A ALA* 3.0 24.6 + - - +
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Residues in contact with ILE 147 (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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41A VAL* 4.9 1.4 - - - +
44A PRO* 3.6 30.2 - - + +
143A ILE* 3.4 25.8 + - + +
144A VAL* 3.1 22.1 + - + +
146A LYS* 1.3 78.5 - - + +
148A PHE* 1.3 66.7 + - + +
150A ALA* 3.3 13.1 + - - +
151A ALA* 3.4 11.1 + - - +
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Residues in contact with PHE 148 (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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44A PRO* 3.7 33.0 - - + -
45A ILE* 3.8 34.3 - - + -
48A VAL* 3.9 9.9 - - + -
132A TYR* 3.6 39.0 - + + +
136A LEU* 4.1 13.0 - - + -
140A HIS* 3.4 24.5 - + - -
144A VAL* 3.0 36.2 + - + +
145A GLN 3.9 0.2 - - - +
147A ILE* 1.3 78.0 - - + +
149A GLN* 1.3 62.1 + - - +
151A ALA* 3.0 9.1 + - - +
152A LEU* 2.9 32.9 + - + +
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Residues in contact with GLN 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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132A TYR* 5.5 1.7 - - + -
145A GLN* 2.8 22.7 + - - +
146A LYS* 3.3 23.7 + - - +
148A PHE* 1.3 73.8 - - - +
150A ALA* 1.3 62.8 + - - +
152A LEU* 3.8 13.1 - - + +
153A TYR* 3.0 26.5 + - + +
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Residues in contact with ALA 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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41A VAL* 3.4 18.5 - - + +
146A LYS 3.0 13.1 + - - +
147A ILE* 3.5 11.9 - - - +
148A PHE 3.2 0.2 - - - -
149A GLN* 1.3 79.3 - - - +
151A ALA* 1.3 62.0 + - - +
153A TYR* 3.6 5.5 + - - +
154A ALA* 3.2 18.7 + - - +
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Residues in contact with ALA 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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41A VAL* 3.0 37.3 - - - +
42A PHE* 3.2 27.1 - - - -
44A PRO* 5.0 2.5 - - + -
45A ILE* 3.7 25.1 - - + -
147A ILE 3.4 5.6 + - - +
148A PHE* 3.0 10.9 + - - +
150A ALA* 1.3 76.7 - - - +
152A LEU* 1.3 65.0 + - - +
154A ALA 3.2 4.9 + - - -
155A ALA* 3.4 1.4 + - - +
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Residues in contact with LEU 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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45A ILE* 4.5 13.7 - - + -
103A PHE* 4.2 22.0 - - + -
125A ARG* 3.9 13.3 - - - +
128A ALA* 4.1 27.1 - - + +
129A THR* 4.4 15.9 - - + +
132A TYR* 3.6 41.3 - - + -
148A PHE* 2.9 20.7 + - + +
149A GLN* 3.8 11.4 - - + +
151A ALA* 1.3 76.9 - - - +
153A TYR* 1.3 62.0 + - - +
155A ALA* 3.4 20.5 + - - +
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Residues in contact with TYR 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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125A ARG* 3.2 68.7 + - - +
149A GLN* 3.0 20.9 + - + +
150A ALA* 3.9 5.6 - - - +
151A ALA 3.2 0.4 - - - -
152A LEU* 1.3 78.5 - - - +
154A ALA* 1.3 57.3 + - - +
155A ALA 3.3 3.1 + - - +
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Residues in contact with ALA 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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39A SER* 5.4 0.2 - - - +
41A VAL* 4.3 18.8 - - + -
42A PHE* 3.1 23.5 - - + -
150A ALA 3.2 16.1 + - - +
151A ALA 3.2 5.5 + - - +
153A TYR* 1.3 76.5 - - - +
155A ALA* 1.3 66.6 + - - +
156A PRO* 3.5 1.0 - - - +
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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