Contacts of the helix formed by residues 148 - 155 (chain A) in PDB entry 2EF1
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 THR 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A TYR* 3.5 2.2 - - - -
115A GLN* 3.3 14.8 - - + +
117A VAL* 4.0 17.9 - - + -
143A PHE* 5.6 1.8 - - + -
144A THR 4.0 3.8 - - - +
145A LEU* 2.7 26.8 + - - +
147A ASP* 1.3 80.4 - - + +
149A LEU* 1.3 65.2 + - - +
150A LEU* 3.9 5.2 + - - +
151A GLY* 3.2 11.6 + - - -
152A TYR* 2.8 22.7 + - - +
196A PHE* 3.7 31.9 - - + -
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Residues in contact with LEU 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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67A CYS* 4.4 11.7 - - - +
70A TYR* 3.4 46.3 + - + -
71A THR* 4.9 2.7 - - + -
77A MET* 4.1 19.3 - - + -
80A VAL* 4.1 24.7 - - + -
85A VAL* 5.1 4.7 - - + -
112A LEU 4.9 0.4 - - - +
113A GLY* 4.5 17.3 - - - +
115A GLN* 2.9 18.0 - - - +
148A THR* 1.3 68.5 - - - +
150A LEU* 1.3 67.3 + - + +
152A TYR* 3.0 5.2 + - - +
153A LEU* 2.9 51.1 + - + +
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Residues in contact with LEU 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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85A VAL* 5.5 0.7 - - + -
109A LEU* 3.9 33.0 - - + +
110A MET* 3.3 35.4 - - + +
113A GLY* 3.9 39.7 - - - +
115A GLN* 4.9 0.4 - - - +
145A LEU* 6.2 0.7 - - + -
148A THR* 3.4 5.5 + - - +
149A LEU* 1.3 80.5 - - + +
151A GLY* 1.3 62.8 + - - +
153A LEU* 3.2 23.4 + - + +
154A ALA 3.3 9.7 + - - -
188A PHE* 3.8 13.9 - - + -
192A VAL* 4.4 13.7 - - + -
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Residues in contact with GLY 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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145A LEU* 3.7 22.3 - - - +
146A GLU* 3.8 11.5 - - - -
148A THR* 3.2 8.5 + - - -
150A LEU* 1.3 81.2 - - - +
152A TYR* 1.3 60.8 + - - +
154A ALA 3.7 0.2 + - - -
155A ASP* 3.2 26.7 + - - +
188A PHE* 5.2 0.9 - - - -
189A TRP* 3.9 19.6 - - - -
192A VAL* 6.0 0.2 - - - -
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Residues in contact with TYR 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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66A ARG* 3.2 63.2 + - + -
69A LYS* 3.6 21.3 - - + +
70A TYR* 3.5 31.9 - + + -
73A ILE* 4.8 7.2 - - + +
146A GLU 3.6 16.6 + - - +
147A ASP* 5.5 0.7 - - - -
148A THR 2.8 17.6 + - - +
149A LEU 3.3 4.3 - - - +
151A GLY* 1.3 79.2 - - - +
153A LEU* 1.3 61.5 + - + +
155A ASP* 3.9 4.6 + - - +
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Residues in contact with LEU 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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63A VAL* 3.4 28.7 - - + +
66A ARG* 3.4 13.9 + - + +
67A CYS* 3.3 38.4 - - + +
85A VAL* 3.6 30.7 - - + -
89A PHE* 4.5 16.2 - - + -
109A LEU* 5.2 0.2 - - + -
149A LEU* 2.9 32.8 + - + +
150A LEU* 3.2 18.1 + - + +
152A TYR* 1.3 77.9 - - + +
154A ALA* 1.3 57.3 + - - +
157A LEU* 3.2 22.2 - - - +
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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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59A PHE* 5.7 0.2 - - - -
66A ARG* 4.0 0.4 - - - -
89A PHE* 4.3 6.7 - - + -
150A LEU 3.3 3.7 + - - +
153A LEU* 1.3 78.5 - - - +
155A ASP* 1.3 67.5 + - - +
156A ASP 3.1 1.0 + - - -
157A LEU* 3.0 23.3 + - - +
159A TRP* 3.5 21.9 - - + -
188A PHE* 3.3 39.3 - - + -
189A TRP* 3.7 10.4 - - + -
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Residues in contact with ASP 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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66A ARG* 2.7 33.2 + - - +
129A LYS* 3.3 32.3 + - - -
133A HIS* 4.4 2.4 + - - -
146A GLU* 3.7 26.8 - - + +
151A GLY 3.2 18.9 + - - +
152A TYR* 4.1 5.8 - - - +
153A LEU 3.6 1.8 - - - -
154A ALA* 1.3 73.8 - - - +
156A ASP* 1.3 81.3 + - - +
157A LEU 3.3 0.3 + - - -
189A TRP* 3.9 7.5 - - - -
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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