Contacts of the helix formed by residues 188 - 203 (chain A) in PDB entry 3ELY
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 HIS 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLU* 3.9 16.0 + - - -
154A PRO* 3.1 38.0 + - + -
155A LEU* 4.6 5.6 - - + -
158A ARG* 3.3 34.6 + - + +
185A ALA* 3.5 19.9 - - + +
186A PRO 3.3 1.2 - - - -
187A TYR* 1.3 111.8 + + - +
189A PRO* 1.4 67.0 - - + +
190A ASP* 4.4 2.2 - - + +
191A VAL* 2.9 24.0 + - + +
192A ILE* 2.9 27.4 + - - +
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Residues in contact with PRO 189 (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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6A VAL* 6.4 0.7 - - + -
7A THR* 4.2 16.2 - - + -
10A GLU* 4.4 16.6 - - - +
187A TYR 3.6 6.4 - - - +
188A HIS* 1.4 85.9 - - + +
190A ASP* 1.3 65.1 + - - +
192A ILE* 3.4 11.0 + - + +
193A GLU* 3.0 25.2 + - - +
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Residues in contact with ASP 190 (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 ARG* 3.9 35.7 + - - -
162A MET* 3.8 20.3 - - + +
188A HIS* 3.2 1.9 - - + +
189A PRO* 1.3 78.7 - - - +
191A VAL* 1.3 57.7 + - - +
193A GLU* 3.4 11.3 + - - +
194A LYS* 3.0 28.1 + - - +
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Residues in contact with VAL 191 (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 ARG* 4.3 7.0 - - + +
161A THR* 3.6 36.8 - - + -
162A MET* 4.0 21.1 - - + -
165A LEU* 4.1 6.7 - - + -
183A VAL* 3.7 17.5 - - + -
185A ALA 3.5 19.5 - - - +
186A PRO* 4.0 6.1 - - + -
188A HIS* 2.9 20.9 + - + +
190A ASP* 1.3 73.9 - - + +
192A ILE* 1.3 59.7 + - - +
194A LYS* 3.3 2.0 + - - +
195A LEU* 3.0 31.9 + - + +
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Residues in contact with ILE 192 (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 PRO 3.2 21.5 - - - +
187A TYR 4.6 3.8 - - - +
188A HIS 2.9 21.2 + - - +
189A PRO* 3.6 10.3 - - + +
190A ASP 3.4 0.2 - - - -
191A VAL* 1.3 75.5 - - - +
193A GLU* 1.3 56.7 + - - +
195A LEU* 3.3 7.4 + - + +
196A GLU* 2.9 52.8 + - + +
229A ILE* 4.0 11.2 - - + +
230A THR* 3.7 22.9 - - + +
233A VAL* 3.6 26.7 - - + -
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Residues in contact with GLU 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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189A PRO 3.0 17.4 + - - +
190A ASP* 3.6 10.6 - - - +
192A ILE* 1.3 77.0 - - - +
194A LYS* 1.3 62.2 + - - +
196A GLU* 3.6 14.5 + - - +
197A ARG* 3.2 23.9 + - + +
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Residues in contact with LYS 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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162A MET* 3.9 22.7 - - + -
165A LEU* 3.8 24.9 - - + -
166A GLU* 3.8 39.6 + - - +
169A GLU* 3.1 20.5 + - - -
190A ASP 3.0 16.9 + - - +
191A VAL 3.7 4.9 - - - +
192A ILE 3.3 0.2 - - - -
193A GLU* 1.3 75.7 - - - +
195A LEU* 1.3 57.5 + - - +
197A ARG* 3.1 49.0 + - - +
198A LEU* 3.0 33.1 + - + +
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Residues in contact with LEU 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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165A LEU* 4.1 20.4 - - + -
183A VAL* 4.0 22.0 - - + -
186A PRO* 4.9 3.4 - - + -
191A VAL* 3.0 34.8 + - + +
192A ILE* 3.6 6.3 - - + +
194A LYS* 1.3 74.0 - - - +
196A GLU* 1.3 59.7 + - - +
198A LEU* 3.3 6.6 + - + +
199A GLN* 2.9 30.9 + - - +
206A ILE* 3.8 26.9 - - + -
221A TYR* 4.3 25.7 + - + -
229A ILE* 3.9 27.5 - - + +
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Residues in contact with GLU 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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192A ILE* 2.9 31.1 + - + +
193A GLU* 3.9 13.9 - - - +
195A LEU* 1.3 75.3 - - - +
197A ARG* 1.3 62.3 + - - +
199A GLN* 3.4 15.0 + - - +
200A LEU* 3.1 29.9 + - + +
228A ASN* 5.5 0.2 - - - +
229A ILE* 4.5 14.4 - - + -
230A THR* 3.2 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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169A GLU* 3.5 24.1 + - - +
193A GLU* 3.2 15.1 + - + +
194A LYS* 3.1 49.6 - - - +
196A GLU* 1.3 77.3 - - - +
198A LEU* 1.3 66.8 + - - +
200A LEU* 3.3 28.9 + - + +
201A ARG* 3.6 12.8 + - + +
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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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165A LEU* 4.2 38.8 - - + +
168A PHE* 4.4 6.5 - - + -
169A GLU* 3.5 41.7 - - + +
194A LYS* 3.0 26.7 + - + +
195A LEU* 3.3 7.4 + - - +
197A ARG* 1.3 78.0 - - - +
199A GLN* 1.3 52.9 + - - +
201A ARG* 3.2 4.9 + - - -
202A PHE* 2.8 57.3 + - + +
221A TYR* 3.6 24.7 - - + +
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Residues in contact with GLN 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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195A LEU 2.9 16.5 + - - +
196A GLU* 3.6 12.6 + - - +
197A ARG 3.3 0.2 - - - -
198A LEU* 1.3 74.7 - - - +
200A LEU* 1.3 61.8 + - - +
203A GLY* 2.8 32.0 + - - +
204A GLY 2.9 28.8 - - - +
205A GLY* 4.2 0.2 - - - -
221A TYR* 3.6 13.6 + - + +
226A ARG* 5.7 1.0 - - + +
227A ASN 3.1 23.6 + - - +
228A ASN* 5.6 0.4 - - - +
229A ILE* 3.8 28.3 - - + +
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Residues in contact with LEU 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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196A GLU* 3.1 22.1 + - + +
197A ARG* 3.5 18.8 - - + +
198A LEU 3.3 0.4 - - - -
199A GLN* 1.3 78.2 - - - +
201A ARG* 1.3 63.0 + - + +
203A GLY 4.9 0.2 + - - -
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Residues in contact with ARG 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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169A GLU* 4.7 15.6 + - - +
197A ARG* 3.6 12.3 + - + +
198A LEU* 3.2 8.1 + - - +
200A LEU* 1.3 81.7 - - + +
202A PHE* 1.3 93.0 + - + +
203A GLY 3.7 0.4 - - - -
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Residues in contact with PHE 202 (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 PHE* 4.0 17.9 - + - -
169A GLU* 4.3 20.9 - - + -
172A LYS* 3.5 52.4 - - + +
179A PHE* 4.1 15.1 - - + -
198A LEU* 2.8 49.4 + - + +
201A ARG* 1.3 106.2 - - + +
203A GLY* 1.3 61.4 + - - +
204A GLY 3.9 0.5 + - - -
221A TYR* 3.7 9.6 - - - +
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Residues in contact with GLY 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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179A PHE* 4.2 0.8 - - - -
199A GLN* 2.8 24.0 + - - -
200A LEU 4.9 0.2 + - - -
201A ARG 3.7 0.8 - - - -
202A PHE* 1.3 78.5 - - - +
204A GLY* 1.3 65.1 + - - +
221A TYR* 2.7 29.3 + - - -
226A ARG* 5.4 5.8 - - - -
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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