Contacts of the helix formed by residues 198 - 208 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B PHE* 3.9 26.7 - - + -
57B THR* 5.0 4.9 - - + -
128B LEU* 4.6 5.1 - - + +
145B VAL* 4.0 16.8 - - + +
148B LYS* 3.3 63.3 - - + +
149B LYS 3.7 15.3 - - - +
150B VAL* 4.0 8.7 - - + +
196B GLU 3.4 0.4 + - - -
197B GLY* 1.3 71.0 - - - -
199B GLY* 1.3 61.6 + - - +
200B SER 3.2 0.4 - - - -
201B VAL* 3.3 23.3 + - + +
202B ASP 3.6 3.3 + - - -
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Residues in contact with GLY 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 5.7 0.7 - - - -
196B GLU* 2.9 16.2 + - - -
197B GLY 2.9 2.4 + - - -
198B LEU* 1.3 78.1 - - - +
200B SER* 1.3 63.4 + - - +
202B ASP* 3.2 12.0 + - - +
203B TYR* 3.0 22.4 + - - +
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B VAL* 3.7 17.0 - - - +
189B CYS 4.8 1.0 + - - -
192B TRP* 3.4 45.7 + - - -
193B ALA* 3.8 2.1 + - - -
196B GLU* 3.7 9.7 - - - +
197B GLY 2.7 17.7 + - - -
199B GLY* 1.3 78.9 - - - +
201B VAL* 1.3 57.7 + - - +
203B TYR* 3.4 10.5 + - - +
204B TYR* 2.8 28.8 + - - +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 3.8 18.2 - - + -
56B LEU* 5.2 0.2 - - + -
71B TYR* 4.0 18.4 - - + +
145B VAL* 4.2 16.4 - - + -
149B LYS 5.0 0.2 - - - +
150B VAL* 3.8 29.2 - - + -
151B PRO* 4.0 14.6 - - + -
198B LEU* 3.3 19.3 + - + +
199B GLY 3.1 0.2 - - - -
200B SER* 1.3 75.7 + - - +
202B ASP* 1.3 66.7 + - - +
204B TYR* 3.1 8.6 + - - +
205B ILE* 2.9 35.4 + - + +
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Residues in contact with ASP 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 3.3 46.9 - - + -
198B LEU 3.6 0.6 + - - -
199B GLY* 3.2 15.5 + - - +
201B VAL* 1.3 80.0 - - - +
203B TYR* 1.3 59.1 + - - +
205B ILE* 3.3 0.7 + - - +
206B ASN* 2.9 61.4 + - - +
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Residues in contact with TYR 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B TRP* 3.9 33.3 - + - -
196B GLU* 6.5 0.2 - - + -
199B GLY 3.0 9.2 + - - +
200B SER* 3.5 9.6 - - - +
202B ASP* 1.3 81.3 - - - +
204B TYR* 1.3 59.0 + - - +
207B GLU* 2.4 76.0 + - + +
208B LEU* 3.3 24.4 + - + +
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Residues in contact with TYR 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG* 3.6 1.9 + - - -
71B TYR* 3.9 31.9 - + - -
74B ASP* 3.2 21.8 + - + -
75B PHE* 3.5 17.0 - + - -
78B ASP* 2.4 31.2 + - - +
185B PHE* 3.7 26.9 - + - -
189B CYS* 5.7 1.8 - - - -
192B TRP* 6.0 2.0 - - + -
200B SER 2.8 14.7 + - - +
201B VAL* 3.1 10.7 + - - +
203B TYR* 1.3 76.7 - - - +
205B ILE* 1.3 65.7 + - + +
208B LEU* 3.0 47.5 + - + +
209B VAL* 3.1 28.6 + - + +
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Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B LEU* 3.5 36.8 - - + -
53B PHE* 3.8 36.6 - - + +
56B LEU* 3.9 14.1 - - + -
71B TYR* 3.7 34.8 - - + -
201B VAL* 2.9 20.6 + - + +
202B ASP 3.8 3.4 - - - +
204B TYR* 1.3 75.9 - - + +
206B ASN* 1.3 64.4 + - - +
209B VAL* 3.8 4.0 - - - +
210B HIS* 2.7 41.1 + - + +
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Residues in contact with ASN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B SER* 3.3 27.0 + - - -
52B LEU 4.6 0.9 + - - -
53B PHE* 3.8 17.8 - - - +
202B ASP* 2.9 42.8 + - - +
203B TYR* 5.0 0.2 - - - -
205B ILE* 1.3 83.7 - - - +
207B GLU* 1.3 75.8 + - - +
210B HIS* 3.4 27.2 - - - +
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B TYR* 2.4 67.8 + - + +
206B ASN* 1.3 89.6 - - - +
208B LEU* 1.3 63.2 + - - +
209B VAL 3.6 0.4 - - - -
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG* 5.6 2.3 + - - -
185B PHE* 5.7 1.8 - - + -
188B GLN* 4.3 8.7 - - - +
192B TRP* 3.5 33.7 - - + -
203B TYR* 3.3 26.5 + - + +
204B TYR* 3.0 41.8 + - + +
207B GLU* 1.3 86.8 - - - +
209B VAL* 1.3 63.5 + - - +
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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