Contacts of the helix formed by residues 189 - 199 (chain A) in PDB entry 2E52
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 GLU 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A PHE* 4.7 6.2 - - - +
102A ASN 5.1 0.5 + - - -
103A TYR* 3.5 29.6 + - + +
138A TYR* 2.6 37.7 + - + +
187A SER* 3.0 18.4 + - - +
188A PHE* 1.3 76.8 - - - +
190A GLN* 1.3 69.4 + - + +
192A TRP* 3.2 24.0 + - - +
193A ASN* 3.2 11.1 + - - +
190D GLN* 3.5 27.2 + - - +
197D LYS* 2.7 28.9 + - - -
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Residues in contact with GLN 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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138A TYR* 4.8 0.6 + - - -
187A SER* 5.0 1.8 + - - -
188A PHE 3.3 1.0 - - - -
189A GLU* 1.3 83.3 - - + +
191A LEU* 1.3 63.8 + - - +
193A ASN* 2.9 27.7 + - - +
194A PHE 3.2 9.5 + - - -
197A LYS* 2.8 25.7 + - - +
218A TYR* 2.5 34.5 + - + +
222A LEU* 4.2 14.6 - - + -
101D PHE* 6.4 1.6 - - + -
102D ASN* 6.4 1.1 - - + -
138D TYR* 4.6 0.6 + - - -
189D GLU* 3.5 34.6 + - - +
190D GLN* 3.7 18.6 - - - +
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Residues in contact with LEU 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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165A LEU* 3.8 8.0 - - + +
167A PHE* 4.1 18.8 - - + -
175A LEU* 4.2 5.4 - - + -
188A PHE* 2.9 15.4 + - + +
190A GLN* 1.3 77.2 - - - +
192A TRP* 1.3 96.8 + - + +
194A PHE* 3.1 20.1 + - - +
215A PHE* 3.8 33.0 - - + -
218A TYR* 4.4 5.4 - - + -
219A PHE* 4.4 3.4 - - + -
222A LEU* 3.6 20.8 - - + +
223A PHE* 3.7 30.5 - - + -
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Residues in contact with TRP 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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75A PHE* 3.5 32.3 - + - -
78A LEU* 4.2 13.7 - - + -
80A LEU* 4.5 6.0 - - + +
103A TYR* 3.0 46.2 + + - -
105A LEU* 3.7 12.5 - - + +
138A TYR* 3.6 34.2 - + + +
139A ALA 4.8 1.7 - - - +
140A VAL* 3.6 22.7 - - + -
163A ASN* 4.1 4.3 - - - +
165A LEU* 3.8 24.4 + - + +
167A PHE* 4.4 13.9 - + - -
188A PHE* 3.4 37.2 + + + -
189A GLU* 3.2 6.2 + - - +
191A LEU* 1.3 95.5 - - + +
193A ASN* 1.3 57.6 + - - +
194A PHE 3.3 1.8 + - - -
195A PRO* 3.7 10.4 - - - +
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Residues in contact with ASN 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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138A TYR* 3.5 21.4 + - + -
163A ASN* 3.0 24.6 + - - -
189A GLU 3.2 14.3 + - - +
190A GLN* 2.9 33.1 + - - +
191A LEU 3.1 1.0 - - - -
192A TRP* 1.3 77.0 - - - +
194A PHE* 1.3 64.9 + - - +
195A PRO* 3.4 3.4 - - - -
196A LYS* 3.2 25.2 + - - +
197A LYS* 3.3 19.2 + - - +
218A TYR* 4.5 0.9 - - - -
138D TYR* 4.6 5.7 + - - -
193D ASN* 6.1 0.8 - - - +
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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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165A LEU* 4.0 10.5 - - + -
166A LEU 6.0 0.2 - - - -
190A GLN 3.2 6.9 + - - -
191A LEU 3.1 16.4 + - - +
193A ASN* 1.3 76.1 - - - +
195A PRO* 1.3 73.8 - - + +
197A LYS* 3.0 3.6 + - - +
198A GLN* 2.7 67.8 + - + +
211A PHE* 4.1 24.2 - + - -
214A ASP 4.3 0.7 - - - -
215A PHE* 3.7 45.1 - + + -
218A TYR* 3.4 55.9 - + + -
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Residues in contact with PRO 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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159A SER* 3.4 31.9 - - - +
160A LEU* 3.5 15.1 - - + +
163A ASN* 3.3 16.4 - - - +
164A VAL 3.4 29.6 - - - +
165A LEU* 3.6 9.0 - - + -
166A LEU 5.0 0.2 - - - +
192A TRP 3.7 8.7 - - - +
193A ASN 3.4 0.7 - - - -
194A PHE* 1.3 103.7 - - + +
196A LYS* 1.3 54.9 + - - +
198A GLN* 4.2 0.4 - - + -
199A SER* 2.8 32.3 + - - -
211A PHE* 5.9 0.2 - - + -
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Residues in contact with LYS 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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160A LEU 5.2 2.2 - - - -
163A ASN* 3.0 29.3 + - + +
193A ASN* 3.2 31.1 + - - +
195A PRO* 1.3 74.4 - - - +
197A LYS* 1.3 62.6 + - + +
199A SER* 2.5 28.1 + - - +
200A LYS* 3.6 18.8 + - + +
137D ASP* 5.6 4.0 - - + +
196D LYS* 4.2 27.3 - - - +
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Residues in contact with LYS 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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190A GLN* 2.8 28.0 + - - +
193A ASN* 3.3 11.4 + - - +
194A PHE 3.0 7.7 + - - +
196A LYS* 1.3 74.4 - - + +
198A GLN* 1.3 65.8 + - - +
200A LYS* 3.2 21.9 + - - +
201A LYS* 3.9 6.6 + - - +
218A TYR* 3.8 28.0 + - + +
102D ASN* 3.0 36.8 + - - +
103D TYR* 4.2 0.2 - - - -
137D ASP* 3.3 27.6 - - - +
138D TYR* 4.2 4.5 - - - -
189D GLU* 2.7 31.8 + - - -
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Residues in contact with GLN 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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160A LEU* 3.6 18.8 - - + -
194A PHE* 2.7 55.4 + - + +
195A PRO* 3.7 3.8 - - + +
197A LYS* 1.3 74.3 - - - +
199A SER* 1.3 60.2 + - - +
201A LYS* 3.1 33.5 + - - +
202A THR* 2.9 32.0 + - - +
211A PHE* 3.8 15.6 - - + +
214A ASP* 2.9 35.9 + - - +
218A TYR* 5.6 0.9 - - - -
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Residues in contact with SER 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 3.9 29.8 - - - +
195A PRO 2.8 17.6 + - - -
196A LYS* 2.5 31.7 + - - +
198A GLN* 1.3 73.5 - - - +
200A LYS* 1.3 67.1 + - - +
201A LYS 3.3 0.7 + - - -
202A THR* 3.3 23.8 + - - +
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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