Contacts of the helix formed by residues 182 - 193 (chain A) in PDB entry 1EQB
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 ASP 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A TYR* 2.9 24.2 + - + +
180A VAL* 3.9 1.7 + - - -
181A VAL* 1.3 71.3 - - - +
183A TRP* 1.3 61.0 + - - +
184A ALA* 3.3 11.1 + - - +
185A LYS* 2.7 44.2 + - + +
186A MET* 3.1 23.4 + - - +
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Residues in contact with TRP 183 (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 GLY* 4.2 12.1 - - - -
173A GLY* 4.5 10.3 - - - -
174A PHE* 4.7 3.6 - + - -
181A VAL* 3.1 43.2 + - + -
182A ASP* 1.3 71.0 - - - +
184A ALA* 1.3 64.3 + - - +
186A MET* 3.1 9.7 + - - +
187A ARG* 2.9 23.2 + - - +
197A LEU* 3.7 5.4 - - + +
199A VAL* 3.7 36.3 - - + -
200A ASP 5.5 0.9 - - - -
201A MET* 5.4 1.1 - - + -
204A VAL* 5.1 7.6 - - + -
213A TYR* 3.9 20.4 - + - -
214A PRO* 2.8 39.5 + - + +
215A ASN 3.6 5.4 - - - -
216A PRO* 3.3 37.3 - - + +
219A HIS* 3.9 20.9 - + + -
220A ALA* 6.5 0.2 - - + -
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Residues in contact with ALA 184 (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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182A ASP* 3.3 7.3 + - - +
183A TRP* 1.3 78.3 - - - +
185A LYS* 1.3 58.8 + - - +
187A ARG* 3.3 5.2 + - - +
188A GLU* 3.0 32.2 + - - +
219A HIS* 3.6 33.0 - - + +
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Residues in contact with LYS 185 (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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155A TYR* 3.9 35.0 - - + -
159A GLU* 4.0 19.6 + - - -
182A ASP* 2.7 39.3 + - + +
184A ALA* 1.3 70.4 - - - +
186A MET* 1.3 65.3 + - - +
188A GLU* 3.3 34.5 + - - +
189A ILE* 3.2 33.0 + - + +
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Residues in contact with MET 186 (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 TYR* 3.6 24.7 - - + +
153A ILE* 5.7 2.2 - - + -
155A TYR* 4.1 14.8 - - + -
158A LEU* 3.9 17.7 - - + -
170A ILE* 3.9 26.3 - - + +
172A GLY* 3.9 20.6 - - - -
181A VAL* 3.6 25.8 - - - -
182A ASP 3.1 11.4 + - - +
183A TRP* 3.1 13.2 + - - +
185A LYS* 1.3 73.6 - - - +
187A ARG* 1.3 60.7 + - - +
189A ILE* 3.3 10.8 + - - +
190A ALA* 2.9 27.5 + - - +
197A LEU* 3.9 16.6 - - + +
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Residues in contact with ARG 187 (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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183A TRP 2.9 11.9 + - - +
184A ALA* 3.5 9.9 - - - +
185A LYS 3.2 0.2 - - - -
186A MET* 1.3 76.0 - - - +
188A GLU* 1.3 66.2 + - - +
190A ALA* 3.3 2.0 + - - -
191A ASP* 2.8 51.4 + - - +
197A LEU* 3.5 8.9 - - + +
218A PRO 5.1 1.8 + - - -
219A HIS* 2.6 61.3 + - + +
220A ALA 4.1 6.1 + - - +
221A HIS* 3.5 38.9 + - - +
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Residues in contact with GLU 188 (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 ALA* 3.0 16.4 + - + +
185A LYS* 3.3 42.0 + - + +
186A MET 3.2 0.2 - - - -
187A ARG* 1.3 78.1 - - - +
189A ILE* 1.3 64.5 + - + +
191A ASP* 3.2 7.9 + - - +
192A SER* 3.1 21.9 + - - -
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Residues in contact with ILE 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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155A TYR* 3.7 26.5 - - + +
158A LEU* 3.7 29.2 - - + +
159A GLU* 3.9 28.7 - - + +
162A ALA* 3.6 29.2 - - + -
170A ILE* 3.9 9.6 - - + -
185A LYS* 3.2 21.9 + - + +
186A MET* 3.5 9.0 - - - +
187A ARG 3.3 0.2 - - - -
188A GLU* 1.3 76.8 - - + +
190A ALA* 1.3 60.4 + - - +
192A SER* 2.6 25.1 + - - +
193A ILE* 3.7 7.4 + - - +
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Residues in contact with ALA 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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170A ILE* 4.2 15.0 - - + -
186A MET 2.9 16.7 + - - +
187A ARG* 3.6 8.5 - - - +
188A GLU 3.2 0.2 - - - -
189A ILE* 1.3 77.5 - - - +
191A ASP* 1.3 63.3 + - - +
193A ILE* 3.0 5.6 + - - +
194A GLY 2.9 4.3 + - - -
195A ALA* 2.9 45.7 + - + +
196A TYR 4.5 0.7 - - - -
197A LEU* 4.2 21.5 - - + +
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Residues in contact with ASP 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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187A ARG* 2.8 54.7 + - - +
188A GLU* 3.5 7.7 - - - +
190A ALA* 1.3 77.7 - - - +
192A SER* 1.3 61.1 + - - +
193A ILE 3.2 1.0 + - - -
194A GLY* 3.2 12.3 + - - +
195A ALA 4.9 1.3 - - - +
221A HIS* 4.4 6.1 + - - -
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Residues in contact with SER 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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159A GLU* 5.4 1.9 - - - +
162A ALA* 5.9 0.2 - - - +
163A LYS* 3.7 26.2 + - - +
188A GLU 3.1 10.4 + - - -
189A ILE* 2.6 27.3 + - - +
191A ASP* 1.3 77.3 - - - +
193A ILE* 1.3 64.1 + - - +
194A GLY 3.5 0.2 - - - -
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Residues in contact with ILE 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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162A ALA* 3.6 27.6 - - + +
163A LYS* 4.2 19.3 - - + +
166A LYS* 4.3 10.3 - - + +
167A PRO* 3.4 49.1 - - + +
170A ILE* 4.4 2.2 - - + -
189A ILE 3.8 6.3 - - - +
190A ALA 3.4 10.5 - - - +
192A SER* 1.3 87.8 + - - +
194A GLY* 1.3 62.7 + - - +
195A ALA* 3.8 9.4 - - + +
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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
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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