Contacts of the helix formed by residues 157 - 179 (chain A) in PDB entry 3EIJ
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 LEU 157 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLU* 5.8 2.5 - - - +
156A PHE* 1.3 77.1 - - - +
158A PRO* 1.3 76.8 - - + +
159A LEU* 2.9 15.0 + - + +
160A ASP* 2.9 26.6 + - + +
161A GLU* 3.0 10.5 + - - +
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Residues in contact with PRO 158 (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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156A PHE 3.7 4.2 - - - +
157A LEU* 1.3 90.9 - - + +
159A LEU* 1.3 60.4 + - - +
161A GLU* 3.8 16.2 - - + +
162A ARG* 3.2 22.7 + - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 2.9 9.3 + - + +
158A PRO* 1.3 80.1 - - - +
160A ASP* 1.3 73.8 + - - +
162A ARG* 3.3 7.5 + - + +
163A ALA* 3.2 21.3 + - + +
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Residues in contact with ASP 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 4.7 16.0 - - + -
157A LEU* 2.9 19.6 + - - +
159A LEU* 1.3 90.6 - - - +
161A GLU* 1.3 64.3 + - - +
163A ALA* 3.9 8.4 - - - +
164A PHE* 3.1 23.7 + - - +
196A MET* 3.7 15.8 - - + +
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 4.7 17.5 - - + +
157A LEU 3.0 13.6 + - - +
158A PRO* 3.8 15.9 - - + +
160A ASP* 1.3 78.5 - - - +
162A ARG* 1.3 55.9 - - - +
164A PHE* 3.6 9.6 - - + +
165A GLU* 3.1 43.3 + - + +
196A MET* 5.1 2.9 - - - -
242A LYS* 3.8 21.1 + - - -
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Residues in contact with ARG 162 (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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158A PRO 3.2 18.0 + - - +
159A LEU* 3.6 6.5 - - + +
160A ASP 3.2 0.2 - - - -
161A GLU* 1.3 74.7 - - - +
163A ALA* 1.3 60.3 + - - +
164A PHE 3.2 1.3 - - - -
165A GLU* 3.4 33.6 + - - +
166A LYS* 2.8 63.2 + - + +
169A THR* 5.8 0.4 + - - -
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Residues in contact with ALA 163 (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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159A LEU* 3.2 13.3 + - + +
160A ASP* 4.0 9.0 - - - +
162A ARG* 1.3 78.8 - - - +
164A PHE* 1.3 55.7 + - - +
166A LYS* 3.8 7.9 - - - +
167A THR* 2.7 38.2 + - - +
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Residues in contact with PHE 164 (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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160A ASP 3.1 18.6 + - - +
161A GLU* 3.6 11.4 - - + +
163A ALA* 1.3 73.6 - - - +
165A GLU* 1.3 68.2 + - + +
167A THR* 3.3 1.9 + - - -
168A LEU* 2.9 68.5 + - + +
193A LEU* 4.2 11.4 - - + -
196A MET* 3.4 44.6 - - + -
199A GLY* 3.4 41.1 - - - -
200A VAL* 3.6 5.8 - - + -
203A LEU* 4.3 15.0 - - + -
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Residues in contact with GLU 165 (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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161A GLU* 3.1 27.6 + - + +
162A ARG* 3.7 27.6 + - - +
164A PHE* 1.3 83.5 - - + +
166A LYS* 1.3 62.2 + - - +
169A THR* 2.7 38.5 + - - +
203A LEU* 4.3 26.5 - - + +
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Residues in contact with LYS 166 (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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162A ARG* 2.8 47.2 + - + +
163A ALA* 3.8 6.7 - - - +
165A GLU* 1.3 78.0 - - - +
167A THR* 1.3 58.5 + - - +
169A THR* 4.7 0.8 - - - -
170A PRO* 3.1 24.8 - - - +
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Residues in contact with THR 167 (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 ALA* 2.7 23.5 + - - +
164A PHE* 3.9 3.1 - - - -
166A LYS* 1.3 79.4 - - - +
168A LEU* 1.3 62.1 + - + +
170A PRO* 3.3 12.2 - - - +
171A ILE* 3.2 25.5 - - + +
191A LEU* 4.0 36.1 - - + -
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Residues in contact with LEU 168 (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 PHE* 2.9 50.3 + - + +
167A THR* 1.3 82.2 - - - +
169A THR* 1.3 64.3 + - - +
171A ILE* 3.1 9.0 + - + +
172A ILE* 2.9 28.0 + - + +
188A LEU* 3.9 20.0 - - + -
191A LEU* 3.9 22.2 - - + -
193A LEU* 4.3 5.6 - - + -
200A VAL* 3.6 39.3 - - + -
203A LEU* 3.6 16.4 - - + -
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Residues in contact with THR 169 (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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162A ARG* 5.8 0.3 + - - -
165A GLU* 2.7 28.4 + - - +
166A LYS* 4.7 1.1 - - - -
168A LEU* 1.3 75.7 - - - +
170A PRO* 1.3 63.6 - - + +
172A ILE* 3.2 1.0 + - - +
173A GLN* 2.7 65.1 + - - +
203A LEU* 4.0 13.6 - - - +
207A LEU* 4.0 22.2 - - + +
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Residues in contact with PRO 170 (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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166A LYS 3.1 21.1 - - - +
167A THR* 3.3 14.6 - - - +
169A THR* 1.3 95.0 - - + +
171A ILE* 1.3 59.0 + - + +
173A GLN* 4.2 8.0 - - + +
174A GLU* 3.0 47.9 + - - +
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Residues in contact with ILE 171 (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* 3.2 31.9 - - + +
168A LEU* 3.1 11.7 + - + +
170A PRO* 1.3 81.9 - - + +
172A ILE* 1.3 64.3 + - + +
174A GLU* 3.9 5.4 - - - +
175A TYR* 3.1 26.2 + - - +
178A HIS* 4.9 1.6 - - - -
184A VAL* 3.9 33.9 - - + +
187A MET* 3.6 37.1 - - + +
188A LEU* 4.5 15.3 - - + -
191A LEU* 5.1 7.2 - - + -
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Residues in contact with ILE 172 (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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168A LEU* 2.9 24.1 + - + +
169A THR 3.9 2.2 - - - +
171A ILE* 1.3 79.3 - - + +
173A GLN* 1.3 66.5 + - - +
174A GLU 3.1 0.4 - - - -
175A TYR* 3.3 9.7 + - + +
176A PHE* 3.2 52.0 + - + -
184A VAL* 6.0 1.6 - - + -
200A VAL* 4.2 8.1 - - + +
203A LEU* 3.7 32.5 - - + -
204A ALA* 3.7 36.3 - - + +
207A LEU* 3.9 12.3 - - + -
222A LEU* 5.2 8.5 - - + -
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Residues in contact with GLN 173 (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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169A THR* 2.7 47.4 + - - +
170A PRO* 4.2 5.3 - - + +
172A ILE* 1.3 72.9 - - - +
174A GLU* 1.3 61.2 + - + +
176A PHE* 3.6 26.1 - - + +
177A GLU* 3.9 10.2 + - - +
207A LEU* 4.3 17.0 - - + +
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Residues in contact with GLU 174 (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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170A PRO* 3.0 36.0 + - - +
171A ILE* 3.9 5.7 - - - +
173A GLN* 1.3 74.4 - - - +
175A TYR* 1.3 57.3 + - - +
176A PHE 3.1 1.1 - - - -
177A GLU* 2.6 32.4 + - + +
178A HIS* 2.9 25.0 + - + +
183A GLU* 5.1 5.7 - - - +
187A MET* 5.3 7.2 - - + +
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Residues in contact with TYR 175 (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 ILE 3.1 18.9 + - - +
172A ILE* 3.5 6.5 - - - +
174A GLU* 1.3 73.5 - - - +
176A PHE* 1.3 69.3 + + - +
177A GLU 2.7 7.1 + - - -
178A HIS* 3.5 11.5 - - - -
179A GLY* 2.6 65.4 + - - -
180A ASP 3.9 2.2 - - - -
181A THR* 3.9 14.2 + - - -
184A VAL* 3.6 25.1 - - + -
218A MET* 2.4 55.1 + - + +
219A THR 4.3 0.4 - - - -
221A LYS* 4.0 8.1 - - - +
222A LEU* 3.8 31.1 + - + -
402B LYS* 5.6 2.1 - - - -
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Residues in contact with PHE 176 (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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172A ILE* 3.2 34.9 + - + -
173A GLN* 3.6 21.3 - - + +
174A GLU 3.1 0.2 - - - -
175A TYR* 1.3 97.1 - + - +
177A GLU* 1.3 64.2 + - - +
204A ALA* 4.0 2.5 - - + -
207A LEU* 4.2 7.6 - - + -
208A ALA* 4.0 24.9 - - + -
215A HIS* 3.4 55.0 - + + +
218A MET* 3.5 24.4 - - + +
219A THR* 3.1 27.4 - - - -
222A LEU* 6.1 0.4 - - + -
398B VAL* 3.8 6.6 - - - +
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Residues in contact with GLU 177 (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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173A GLN 4.2 8.8 - - - +
174A GLU* 2.6 25.7 + - + +
175A TYR 2.7 0.4 + - - -
176A PHE* 1.3 84.2 - - - +
178A HIS* 1.3 57.0 + - + -
215A HIS* 4.9 6.9 + - - -
391B TRP* 4.8 4.9 - - - -
398B VAL* 3.2 24.5 - - - +
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Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE 4.9 1.6 - - - -
174A GLU* 2.9 24.5 + - + +
175A TYR* 3.5 28.1 - - + +
177A GLU* 1.3 77.4 - - + +
179A GLY* 1.3 63.7 + - - +
180A ASP* 2.8 58.4 + - + -
183A GLU* 3.7 32.8 + - + +
184A VAL* 4.2 4.9 - - + +
187A MET* 4.9 3.8 - - + -
391B TRP* 6.1 0.2 - - - -
398B VAL* 3.6 14.1 - - - +
440B SER* 4.1 16.1 + - - -
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Residues in contact with GLY 179 (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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175A TYR* 2.6 41.1 + - - -
177A GLU 3.7 0.8 - - - -
178A HIS* 1.3 70.2 - - - +
180A ASP* 1.3 58.4 + - - +
181A THR* 3.2 7.4 + - - -
218A MET* 3.7 13.7 - - - +
398B VAL* 4.9 3.1 - - - -
402B LYS* 3.9 24.2 + - - +
440B SER* 5.2 1.3 - - - -
442B GLN* 3.5 7.4 - - - +
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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
------------------------------------------------------------
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