Contacts of the helix formed by residues 198 - 209 (chain A) in PDB entry 3CEI
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.9 26.7 - - + -
57A THR* 4.9 4.5 - - + -
128A LEU* 4.6 5.3 - - + +
145A VAL* 3.9 13.9 - - + +
148A LYS* 3.3 63.5 - - + +
149A LYS 3.7 14.4 - - - +
150A VAL* 3.9 9.3 - - + +
196A GLU 3.5 0.4 + - - -
197A GLY* 1.3 71.0 - - - -
199A GLY* 1.3 60.7 + - - +
200A SER 3.2 0.7 - - - -
201A VAL* 3.3 23.4 + - + +
202A ASP 3.6 3.1 + - - -
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Residues in contact with GLY 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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53A PHE* 5.7 0.4 - - - -
196A GLU* 2.9 17.3 + - - -
197A GLY 2.8 2.4 + - - -
198A LEU* 1.3 77.2 - - - +
200A SER* 1.3 63.8 + - - +
202A ASP* 3.1 11.6 + - - +
203A TYR* 3.0 22.0 + - - +
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Residues in contact with SER 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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150A VAL* 3.7 17.8 - - - +
189A CYS* 4.9 1.1 + - - -
192A TRP* 3.3 46.0 + - - -
193A ALA* 3.8 1.2 + - - -
196A GLU* 3.7 9.6 - - - +
197A GLY 2.6 19.1 + - - -
199A GLY* 1.3 77.8 - - - +
201A VAL* 1.3 56.6 + - - +
203A TYR* 3.4 10.5 + - - +
204A TYR* 2.8 29.7 + - - +
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Residues in contact with VAL 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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53A PHE* 3.8 18.2 - - + -
56A LEU* 5.3 0.2 - - + -
71A TYR* 4.0 17.9 - - + +
145A VAL* 4.0 16.6 - - + -
150A VAL* 3.7 30.7 - - + -
151A PRO* 4.0 15.3 - - + -
198A LEU* 3.4 17.7 - - + +
199A GLY 3.1 0.2 - - - -
200A SER* 1.3 76.2 + - - +
202A ASP* 1.3 66.5 + - - +
204A TYR* 3.2 7.2 + - - +
205A ILE* 2.9 35.0 + - + +
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Residues in contact with ASP 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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53A PHE* 3.4 40.7 - - + -
198A LEU 3.6 1.4 + - - -
199A GLY* 3.1 16.5 + - - +
201A VAL* 1.3 80.5 - - - +
203A TYR* 1.3 63.8 + - - +
205A ILE* 3.8 0.2 - - - +
206A ASN* 2.6 54.2 + - - +
207A GLU* 5.8 0.3 - - - +
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Residues in contact with TYR 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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192A TRP* 4.0 38.5 - + - -
196A GLU* 6.5 0.4 - - + -
199A GLY 3.0 8.5 + - - +
200A SER* 3.6 9.2 - - - +
202A ASP* 1.3 81.8 - - - +
204A TYR* 1.3 61.0 + - - +
207A GLU* 2.7 79.9 + - + +
208A LEU* 3.4 13.0 + - + +
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Residues in contact with TYR 204 (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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5A ARG* 3.6 1.2 + - - -
71A TYR* 3.9 32.8 - + - -
74A ASP* 3.3 19.7 + - + -
75A PHE* 3.4 21.0 - + - -
78A ASP* 2.4 31.5 + - - +
185A PHE* 3.6 28.9 - + - -
189A CYS* 5.7 2.0 - - - -
192A TRP* 5.9 6.5 - + + -
200A SER 2.8 18.1 + - - +
201A VAL* 3.3 8.1 - - - +
203A TYR* 1.3 80.0 - - + +
205A ILE* 1.3 66.9 + - + +
208A LEU* 2.7 52.2 - - + +
209A VAL* 3.3 21.9 + - + +
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Residues in contact with ILE 205 (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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52A LEU* 3.5 37.7 - - + -
53A PHE* 3.8 34.1 - - + +
56A LEU* 3.9 15.3 - - + -
71A TYR* 3.7 39.0 - - + -
201A VAL* 2.9 16.8 + - + +
202A ASP 3.8 2.2 - - - +
204A TYR* 1.3 80.7 - - + +
206A ASN* 1.3 64.5 + - - +
209A VAL* 3.9 4.2 - - - +
210A HIS* 2.8 36.4 + - + +
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Residues in contact with ASN 206 (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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51A SER* 3.0 32.9 + - - -
52A LEU 3.8 7.8 + - - -
53A PHE* 3.4 17.8 + - - +
202A ASP* 2.6 40.4 + - - +
205A ILE* 1.3 78.2 - - - +
207A GLU* 1.3 71.3 + - + +
210A HIS* 3.7 6.7 - - - +
211A LYS* 3.3 23.8 - - - -
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Residues in contact with GLU 207 (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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202A ASP* 5.8 0.4 - - - +
203A TYR* 2.7 64.8 + - + +
206A ASN* 1.3 85.6 - - + +
208A LEU* 1.3 57.0 + - - +
209A VAL 3.8 0.2 - - - -
211A LYS* 3.6 27.3 + - - +
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Residues in contact with LEU 208 (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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185A PHE* 6.1 1.6 - - + -
188A GLN* 5.1 6.5 - - - +
192A TRP* 4.8 19.5 - - + -
203A TYR* 3.4 15.5 + - + +
204A TYR* 2.7 62.6 + - + +
207A GLU* 1.3 80.1 - - + +
209A VAL* 1.3 68.2 + - + +
211A LYS* 4.1 16.3 + - - +
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Residues in contact with VAL 209 (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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5A ARG* 4.1 33.4 - - + +
74A ASP* 3.9 15.0 - - + +
78A ASP* 4.6 0.9 - - - +
204A TYR* 3.3 43.5 + - + +
205A ILE* 3.9 3.6 - - - +
208A LEU* 1.3 92.6 - - + +
210A HIS* 1.3 84.7 + - + +
211A LYS* 3.4 8.7 + - - +
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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