Contacts of the helix formed by residues 191 - 207 (chain A) in PDB entry 1EFA
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 SER 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A PRO* 4.3 7.6 - - - -
149A ASP* 4.5 2.9 + - - -
188A PRO* 2.9 27.2 + - - -
189A LEU 2.9 0.2 - - - -
190A SER* 1.3 79.0 + - - +
192A VAL* 1.3 66.2 + - - +
193A SER* 3.5 7.1 + - - -
194A ALA* 3.2 19.0 + - - +
195A ARG* 3.0 26.8 + - - +
220A TRP* 3.6 16.0 + - - -
901A NPF 4.2 5.0 + - - -
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PRO* 4.2 4.2 - - + +
128A LEU 3.5 32.5 - - - +
129A ASP* 4.4 1.1 - - - +
149A ASP* 3.6 20.1 + - - +
150A VAL 3.5 31.2 - - - +
151A SER* 3.5 11.9 - - - +
190A SER 3.9 1.2 + - - +
191A SER* 1.3 71.6 + - - +
193A SER* 1.3 60.0 + - - +
195A ARG* 3.1 33.5 + - - +
196A LEU* 2.8 39.6 + - + +
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Residues in contact with SER 193 (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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149A ASP* 3.3 10.3 + - - -
191A SER* 3.3 2.0 - - - -
192A VAL* 1.3 80.1 - - - +
194A ALA* 1.3 63.0 + - - +
196A LEU* 3.3 14.5 + - - +
197A ARG* 3.1 53.2 + - - +
220A TRP* 5.0 0.7 - - - -
901A NPF 3.6 34.4 - - - -
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Residues in contact with ALA 194 (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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186A ALA* 5.1 3.6 - - - +
187A GLY* 3.6 30.0 + - - +
188A PRO 3.2 26.2 - - - +
189A LEU* 5.0 1.8 - - + -
191A SER* 3.1 13.2 + - - +
193A SER* 1.3 79.1 - - - +
195A ARG* 1.3 57.7 - - - +
197A ARG* 3.0 10.1 + - - +
198A LEU* 2.9 27.6 + - - +
220A TRP* 4.0 10.9 - - + -
245A ALA* 5.6 0.6 - - - +
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Residues in contact with ARG 195 (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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129A ASP* 2.8 32.3 + - - +
189A LEU* 2.9 46.3 + - + +
190A SER* 3.9 15.6 + - - +
191A SER 3.0 16.2 + - - +
192A VAL* 3.2 35.2 - - + +
194A ALA* 1.3 76.6 - - - +
196A LEU* 1.3 64.4 + - + +
198A LEU* 3.1 9.0 + - + +
199A ALA* 2.9 25.3 + - - +
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Residues in contact with LEU 196 (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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150A VAL 3.9 21.3 - - - +
151A SER* 3.9 27.6 - - - +
152A ASP* 4.2 1.3 - - - +
160A ILE* 4.2 8.5 - - + -
163A HIS* 3.6 53.7 + - + +
192A VAL* 2.8 29.4 + - + +
193A SER* 3.6 13.9 - - - +
194A ALA 3.2 0.2 - - - -
195A ARG* 1.3 73.9 - - + +
197A ARG* 1.3 58.9 + - - +
199A ALA* 3.4 6.7 + - + +
200A GLY* 2.9 23.6 + - - -
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Residues in contact with ARG 197 (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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163A HIS* 4.7 8.7 - - + -
167A THR* 3.2 17.8 - - + +
193A SER* 3.1 37.9 + - - +
194A ALA* 3.0 8.5 + - - +
196A LEU* 1.3 73.4 - - - +
198A LEU* 1.3 66.7 + - - +
200A GLY 3.1 0.7 + - - -
201A TRP* 3.0 37.3 + - + -
220A TRP* 3.4 15.7 - - - -
245A ALA* 2.6 43.1 + - + +
273A TYR* 3.6 39.7 - - + +
291A GLN* 3.3 20.6 + - - +
901A NPF 3.2 37.2 + - - -
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Residues in contact with LEU 198 (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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184A LEU* 4.1 12.3 - - + -
186A ALA* 3.8 19.7 - - + -
189A LEU* 4.1 26.7 - - + -
194A ALA 2.9 12.9 + - - +
195A ARG* 3.4 10.5 - - + +
197A ARG* 1.3 76.6 - - - +
199A ALA* 1.3 64.2 + - - +
201A TRP* 3.1 13.8 + - + +
202A HIS* 3.0 46.7 + - + +
215A GLU* 3.6 23.1 - - + +
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Residues in contact with ALA 199 (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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163A HIS* 5.9 1.8 - - + +
195A ARG 2.9 16.8 + - - +
196A LEU* 3.6 8.7 - - + +
198A LEU* 1.3 76.6 - - - +
200A GLY* 1.3 57.4 + - - +
202A HIS* 3.1 9.3 + - - +
203A LYS* 2.8 32.3 + - - +
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Residues in contact with GLY 200 (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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163A HIS* 4.9 6.0 + - - -
164A GLU* 5.5 2.9 - - - -
167A THR* 3.3 23.4 + - - -
196A LEU 2.9 14.6 + - - -
197A ARG 3.1 3.3 + - - -
199A ALA* 1.3 77.3 - - - +
201A TRP* 1.3 60.4 + - - +
203A LYS* 4.4 5.8 - - - -
204A TYR* 3.0 34.2 + - - -
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Residues in contact with TRP 201 (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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167A THR* 3.4 36.3 - - + +
170A GLY* 5.7 0.4 - - - -
171A VAL* 4.1 4.6 - - + +
184A LEU* 4.1 32.8 - - + -
185A LEU 3.5 18.8 - - - -
186A ALA* 4.1 12.1 - - + -
197A ARG* 3.0 25.8 + - + -
198A LEU* 3.1 15.7 + - + +
200A GLY* 1.3 71.9 - - - +
202A HIS* 1.3 61.1 + - - +
204A TYR 3.3 0.9 + - - -
205A LEU* 2.8 36.6 + - + +
243A LEU* 3.7 45.6 - - + +
244A VAL 3.5 17.0 - - - -
245A ALA* 3.3 33.2 - - + -
273A TYR* 4.8 10.9 - + - -
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Residues in contact with HIS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 3.8 14.3 - - + +
198A LEU* 3.0 30.0 + - + +
199A ALA* 3.6 9.9 - - - +
201A TRP* 1.3 76.1 - - - +
203A LYS* 1.3 66.3 + - - +
205A LEU* 3.9 2.9 - - + +
206A THR* 2.9 30.2 + - - +
212A PRO* 4.0 18.4 - - + +
215A GLU* 2.6 43.9 + - - -
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Residues in contact with LYS 203 (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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164A GLU* 2.6 32.1 + - - +
199A ALA 2.8 19.6 + - - +
200A GLY* 3.6 6.5 - - - +
202A HIS* 1.3 75.9 - - - +
204A TYR* 1.3 81.6 + - + +
206A THR* 3.3 6.2 + - - +
207A ARG* 3.2 61.3 + - + +
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Residues in contact with TYR 204 (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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164A GLU* 3.0 46.0 + - + +
167A THR* 3.9 8.1 - - - -
168A ARG* 3.4 42.6 + - + -
171A VAL* 3.7 24.1 - - + +
172A GLU* 4.8 4.3 - - + -
200A GLY* 3.0 29.0 + - - +
203A LYS* 1.3 101.6 + - + +
205A LEU* 1.3 63.7 + - - +
206A THR 3.2 0.4 + - - -
207A ARG* 3.5 29.5 + - + +
208A ASN* 2.7 29.3 - - - +
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Residues in contact with LEU 205 (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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171A VAL* 3.7 27.4 - - + -
182A ILE* 3.9 28.3 - - + -
184A LEU* 3.9 32.8 - - + -
201A TRP* 2.8 28.1 + - + +
202A HIS* 3.9 4.0 - - - +
204A TYR* 1.3 74.4 - - - +
206A THR* 1.3 61.7 + - - +
208A ASN* 3.0 9.6 + - - -
210A ILE* 2.9 49.7 + - + +
212A PRO* 4.0 26.0 - - + -
243A LEU* 4.6 2.2 - - + -
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Residues in contact with THR 206 (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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202A HIS* 2.9 21.8 + - - +
203A LYS* 3.4 7.6 - - - +
205A LEU* 1.3 73.7 - - - +
207A ARG* 1.3 61.0 + - + +
208A ASN 2.9 4.7 - - - -
209A GLN* 2.7 25.7 + - - +
210A ILE 4.0 7.3 + - - +
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Residues in contact with ARG 207 (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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203A LYS* 3.2 48.4 + - + +
204A TYR* 3.9 31.3 + - + +
205A LEU 3.3 0.6 - - - -
206A THR* 1.3 79.1 - - + +
208A ASN* 1.3 63.3 + - - +
209A GLN* 3.4 10.0 + - - -
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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