Contacts of the helix formed by residues 186 - 197 (chain A) in PDB entry 2EE4
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 ILE 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LEU* 3.7 16.8 - - + -
111A ALA* 3.4 36.6 - - + +
112A LYS* 4.2 33.4 - - + -
184A THR* 3.1 22.4 + - + +
185A LYS* 1.3 82.2 - - - +
187A HIS* 1.3 61.4 + - - +
188A GLN 2.9 3.1 - - - -
189A SER* 2.6 32.6 + - - +
190A VAL* 2.8 19.5 + - + +
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Residues in contact with HIS 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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104A HIS* 5.9 1.1 - - - -
108A LEU* 3.3 32.0 - - + +
167A TRP* 3.7 42.8 - - + +
171A MET* 4.1 29.3 - - + +
173A PRO* 4.6 19.5 - - + -
175A PHE* 5.2 6.7 - + - -
184A THR* 3.3 27.4 + - - +
185A LYS 3.8 0.2 - - - -
186A ILE* 1.3 75.7 - - - +
188A GLN* 1.3 61.4 + - - +
190A VAL* 3.8 8.3 - - - +
191A VAL* 3.6 23.9 + - - +
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Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP* 4.7 7.5 + - - +
163A SER* 3.2 25.4 + - - +
164A ILE* 3.0 51.0 - - + +
167A TRP* 4.3 19.6 - - + +
185A LYS* 4.8 19.4 - - + +
186A ILE 2.8 2.4 + - - +
187A HIS* 1.3 79.1 - - - +
189A SER* 1.3 66.4 + - - +
191A VAL* 3.6 2.1 + - - +
192A GLU* 3.2 13.4 + - - +
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Residues in contact with SER 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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111A ALA* 5.5 2.9 - - - -
119A ARG* 5.2 9.6 - - - -
185A LYS 4.0 10.9 + - - -
186A ILE* 2.6 22.0 + - - -
188A GLN* 1.3 75.3 + - - +
190A VAL* 1.3 68.2 + - - -
192A GLU* 2.9 26.6 + - - +
193A THR* 2.9 21.2 + - - -
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 6.1 2.5 - - + -
107A LEU* 4.1 26.9 - - + +
108A LEU* 4.2 9.9 - - + -
111A ALA* 3.5 15.0 - - + +
123A LEU* 4.7 6.5 - - + +
171A MET* 5.3 7.9 - - - -
186A ILE* 2.8 44.9 + - + +
187A HIS* 3.8 9.6 - - - +
189A SER* 1.3 72.5 - - - +
191A VAL* 1.3 69.5 + - + +
193A THR* 3.6 5.9 + - - -
194A PHE* 3.2 44.4 + - + -
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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
----------------------------------------------------------
99A ILE* 5.1 9.0 - - + -
138A PHE* 5.8 2.7 - - + -
142A ILE* 4.8 7.0 - - + -
145A LEU* 4.9 0.9 - - + -
163A SER* 3.6 18.2 - - - +
166A PHE* 4.6 1.3 - - + -
167A TRP* 4.1 19.7 - - + -
170A LEU* 4.1 28.7 - - + -
171A MET* 5.4 3.6 - - + -
187A HIS 3.6 14.6 - - - +
188A GLN 3.6 3.3 + - - +
189A SER 3.2 0.6 - - - -
190A VAL* 1.3 75.4 - - + +
192A GLU* 1.3 72.0 + - - +
194A PHE* 2.9 22.4 + - - +
195A ILE* 3.1 27.0 + - + +
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Residues in contact with GLU 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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116A LYS* 5.6 2.4 + - - -
119A ARG* 5.5 2.3 + - - -
159A ALA 4.3 0.4 - - - -
160A ASP* 2.5 44.1 - - - +
163A SER* 3.2 25.2 - - - +
188A GLN* 3.2 11.3 + - + +
189A SER* 2.9 21.1 + - - +
191A VAL* 1.3 72.4 - - - +
193A THR* 1.3 61.7 + - - +
195A ILE* 2.6 29.7 + - - +
196A GLN* 2.8 36.7 + - + +
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Residues in contact with THR 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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111A ALA* 6.1 0.3 - - - +
116A LYS* 5.0 4.9 + - - +
119A ARG* 3.6 28.4 + - - +
120A LEU* 3.3 26.9 - - + -
123A LEU* 4.1 13.9 - - + -
189A SER* 2.9 16.4 + - - -
190A VAL* 3.7 9.1 - - - -
192A GLU* 1.3 80.3 + - - +
194A PHE* 1.3 66.2 + - - +
195A ILE 2.8 0.3 + - - -
196A GLN* 4.5 1.3 - - - -
197A GLN* 2.7 47.7 + - - +
201A PHE* 4.1 4.7 - - + -
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Residues in contact with PHE 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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107A LEU* 4.0 19.7 - - + -
123A LEU* 3.8 20.4 - - + -
127A VAL* 4.0 26.7 - - + -
130A PHE* 5.3 3.4 - + - -
138A PHE* 3.8 24.0 - + - -
142A ILE* 2.8 32.1 - - + +
190A VAL* 3.2 40.8 + - + -
191A VAL* 2.9 15.8 + - - +
193A THR* 1.3 74.6 - - - +
195A ILE* 1.3 56.4 + - - +
198A CYS* 2.8 18.2 - - - -
201A PHE* 3.3 44.9 - + + -
202A PHE* 5.4 2.0 - + - -
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Residues in contact with ILE 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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142A ILE* 3.6 13.0 - - + -
145A LEU* 3.7 30.1 - - + +
146A ASN* 2.5 60.5 + - - +
159A ALA* 3.8 25.4 - - + +
162A LEU* 5.0 0.2 - - + -
163A SER* 3.5 34.8 - - - +
191A VAL* 3.4 20.0 - - + +
192A GLU* 2.6 11.7 + - - +
194A PHE* 1.3 70.9 - - - +
196A GLN* 1.3 59.4 + - - +
197A GLN 3.2 0.9 - - - -
198A CYS* 2.8 11.1 + - - +
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Residues in contact with GLN 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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116A LYS* 4.8 5.5 + - - -
146A ASN* 3.4 13.1 + - - +
149A SER* 5.6 0.7 - - - -
159A ALA* 3.2 27.2 - - + +
160A ASP* 4.4 8.4 + - - +
192A GLU* 2.8 39.4 + - + +
193A THR* 4.5 0.2 - - - -
195A ILE* 1.3 75.1 - - - +
197A GLN* 1.3 77.2 + - - +
198A CYS 3.5 0.9 + - - -
199A GLN* 4.8 3.8 + - - +
206A GLU 5.1 0.2 - - - +
208A VAL* 3.0 30.4 - - + +
209A GLU 3.5 33.1 + - - -
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Residues in contact with GLN 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LYS* 3.6 16.7 + - - +
120A LEU* 3.4 26.5 - - + -
193A THR* 2.7 47.4 + - - +
196A GLN* 1.3 82.6 + - - +
198A CYS* 1.3 66.1 + - - +
199A GLN* 2.7 6.3 + - - -
200A PHE* 2.9 21.4 + - + +
201A PHE* 2.9 26.1 + - + -
206A GLU 5.2 2.5 - - - -
207A ILE* 3.9 11.7 - - + -
208A VAL* 2.8 46.7 + - - +
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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