Contacts of the helix formed by residues 164 - 179 (chain B) in PDB entry 1EF1
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 ASN 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B LEU* 1.3 75.6 - - - +
165B LYS* 1.3 66.4 + - - +
166B ASP* 3.1 16.3 + - - +
167B GLN* 2.7 61.5 + - - +
168B TRP* 2.9 25.2 + - - -
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Residues in contact with LYS 165 (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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147B LEU 5.5 0.2 - - - -
148B ALA* 3.0 39.5 + - - +
150B ASP 5.9 1.8 - - - -
164B ASN* 1.3 76.0 - - + +
166B ASP* 1.3 70.9 + - - +
168B TRP* 3.2 9.0 + - - +
169B GLU* 3.0 51.1 + - - +
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Residues in contact with ASP 166 (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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164B ASN* 3.1 14.5 + - - +
165B LYS* 1.3 83.6 - - - +
167B GLN* 1.3 57.2 + - + +
169B GLU* 3.2 12.4 + - - +
170B GLU* 3.0 45.3 + - - +
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Residues in contact with GLN 167 (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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162B LYS 4.2 2.6 + - - +
163B LEU* 3.2 30.1 - - + +
164B ASN* 2.7 61.7 + - - +
166B ASP* 1.3 71.5 - - + +
168B TRP* 1.3 63.5 + - - +
170B GLU* 3.3 15.1 + - - +
171B ARG* 3.0 32.7 + - - +
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Residues in contact with TRP 168 (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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123B VAL* 3.7 27.4 - - + -
152B LEU* 5.4 2.9 - - + -
153B LEU* 3.8 20.6 - - + -
157B VAL* 4.2 9.9 - - + -
158B LEU* 3.3 34.9 + - + +
161B HIS* 3.6 34.3 - + + +
163B LEU* 3.7 35.6 + - + +
164B ASN 2.9 22.6 + - - -
165B LYS* 3.5 10.1 - - - +
167B GLN* 1.3 76.8 - - - +
169B GLU* 1.3 59.0 + - + +
171B ARG* 3.3 9.6 + - + +
172B ILE* 3.0 46.4 + - + +
529D LEU* 4.0 21.5 - - + -
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Residues in contact with GLU 169 (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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145B GLY* 3.8 20.4 + - - +
146B TYR* 5.4 2.4 - - + -
147B LEU* 3.7 28.0 + - + +
148B ALA* 3.4 27.8 + - - +
152B LEU* 4.4 10.2 - - + +
165B LYS* 3.0 53.9 + - + +
166B ASP* 3.7 11.1 - - - +
168B TRP* 1.3 76.3 - - + +
170B GLU* 1.3 57.7 + - + +
172B ILE* 3.4 2.3 + - - +
173B GLN* 2.8 31.2 + - - +
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Residues in contact with GLU 170 (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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166B ASP* 3.0 31.6 + - - +
167B GLN* 3.3 13.9 + - - +
169B GLU* 1.3 77.8 - - + +
171B ARG* 1.3 64.2 + - + +
173B GLN* 3.4 9.8 + - - +
174B VAL* 3.3 26.3 + - - +
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Residues in contact with ARG 171 (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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123B VAL* 5.9 2.9 - - + -
163B LEU* 3.7 36.1 - - - +
167B GLN* 3.0 22.2 + - - +
168B TRP* 3.8 14.4 - - + +
170B GLU* 1.3 77.8 - - + +
172B ILE* 1.3 63.7 + - + +
174B VAL* 3.2 17.0 + - - +
175B TRP* 3.4 22.7 + - + -
528D GLU* 2.9 46.6 + - - +
529D LEU* 4.0 9.9 - - + +
531D ASN* 5.8 2.2 - - - +
532D ALA* 4.4 13.1 - - - +
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Residues in contact with ILE 172 (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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123B VAL* 4.1 19.5 - - + -
126B ALA* 4.4 8.1 - - + -
127B SER* 4.5 16.2 - - - +
130B VAL* 4.2 17.0 - - + -
147B LEU* 3.8 20.4 - - + -
152B LEU* 3.7 32.3 - - + -
153B LEU* 4.4 10.1 - - + -
168B TRP* 3.0 37.8 + - + +
169B GLU 3.9 2.7 - - - +
171B ARG* 1.3 75.8 - - + +
173B GLN* 1.3 52.4 + - - +
175B TRP* 3.1 8.5 + - - +
176B HIS* 2.7 32.6 + - - +
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Residues in contact with GLN 173 (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 PHE* 3.4 32.3 - - + -
146B TYR* 3.6 33.4 - - + +
169B GLU 2.8 18.8 + - - +
170B GLU* 3.7 11.9 - - - +
171B ARG 3.3 0.4 - - - -
172B ILE* 1.3 73.3 - - - +
174B VAL* 1.3 77.2 + - - +
176B HIS* 3.4 1.2 - - - +
177B GLU* 3.0 44.8 + - - +
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Residues in contact with VAL 174 (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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170B GLU 3.3 15.3 - - - +
171B ARG* 3.2 11.7 + - - +
173B GLN* 1.3 90.1 - - - +
175B TRP* 1.3 65.7 + - + +
177B GLU* 3.3 7.4 - - + +
178B GLU* 3.1 24.4 + - + +
528D GLU* 6.0 2.0 - - - +
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Residues in contact with TRP 175 (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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123B VAL* 4.6 8.7 - - + +
124B LEU* 4.5 6.3 - - + -
127B SER* 3.5 21.8 - - - -
171B ARG* 3.4 24.3 + - + +
172B ILE* 3.1 6.3 + - - +
174B VAL* 1.3 83.6 - - + +
176B HIS* 1.3 66.6 + - - +
178B GLU* 3.0 32.0 + - + +
179B HIS* 3.3 21.5 + + - -
520D LYS* 3.7 19.3 - - - -
521D HIS* 3.4 47.6 - + + -
524D ALA* 3.9 8.5 - - + -
525D LEU* 3.3 33.1 - - + +
528D GLU* 2.9 37.8 + - - -
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Residues in contact with HIS 176 (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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127B SER* 4.1 5.9 - - - -
130B VAL* 3.2 29.9 - - + +
131B GLN* 3.1 26.5 + - - +
134B TYR* 3.8 13.9 - - + -
135B GLY 2.8 26.8 + - - -
137B PHE* 3.5 25.7 + - + +
142B HIS* 4.4 1.3 - - - -
146B TYR* 2.9 29.5 + + - +
172B ILE 2.7 17.1 + - - +
173B GLN 3.4 8.1 - - - +
175B TRP* 1.3 69.8 - - - +
177B GLU* 1.3 64.7 + - - +
179B HIS* 3.1 20.4 + - - +
180B ARG* 3.9 1.0 + - - -
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Residues in contact with GLU 177 (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 PHE* 3.4 34.7 - - + +
173B GLN* 3.0 32.3 + - - +
174B VAL* 3.3 8.7 - - + +
176B HIS* 1.3 80.5 - - - +
178B GLU* 1.3 61.1 + - - +
180B ARG* 3.2 38.7 + - + +
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Residues in contact with GLU 178 (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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174B VAL* 3.1 12.9 + - + +
175B TRP* 3.0 31.4 + - + +
177B GLU* 1.3 76.6 - - - +
179B HIS* 1.3 55.9 + - - +
180B ARG* 3.1 6.0 + - - +
520D LYS* 4.7 8.1 + - - -
521D HIS* 4.0 32.6 - - + +
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Residues in contact with HIS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.3 7.4 - - + -
127B SER* 2.6 52.9 + - - -
128B TYR* 3.6 36.3 - + - -
131B GLN* 3.7 24.3 - - + +
175B TRP* 3.3 24.8 + + - -
176B HIS 3.1 7.9 + - - +
178B GLU* 1.3 79.9 - - + +
180B ARG* 1.3 67.0 + - - +
181B GLY 3.2 0.3 + - - -
182B MSE 3.0 29.5 + - - +
521D HIS* 4.6 7.2 + - - -
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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