Contacts of the strand formed by residues 203 - 212 (chain C) in PDB entry 4AEJ
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 TRP 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C ARG* 3.2 72.8 - - + +
150C HIS* 3.6 22.7 - - + -
151C CYS 3.4 28.7 - - - -
152C LYS* 3.7 24.4 - - + +
202C GLU* 1.3 77.7 - - - +
204C SER* 1.3 62.5 + - - +
234C GLU* 3.1 43.1 - - + -
235C PHE* 3.9 7.2 - - - -
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Residues in contact with SER 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ARG* 5.1 1.2 + - - +
150C HIS* 3.4 7.6 + - - +
151C CYS* 2.8 34.1 + - - -
193C GLU* 4.8 2.8 + - - -
195C GLY* 3.2 35.6 + - - -
202C GLU 3.7 2.2 + - - -
203C TRP* 1.3 76.7 - - - +
205C LYS* 1.3 73.0 + - - +
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Residues in contact with LYS 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C THR* 3.8 20.7 + - + +
149C TYR 3.1 12.1 - - - +
150C HIS* 3.8 20.4 - - + +
151C CYS* 3.8 1.2 - - - -
193C GLU* 3.9 21.6 - - - +
195C GLY* 3.1 20.6 + - - -
196C CYS* 3.5 4.0 - - - -
204C SER* 1.3 87.3 + - - +
206C THR* 1.3 61.7 + - - +
207C VAL* 4.5 16.0 - - + +
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Residues in contact with THR 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C THR* 3.5 2.1 - - - -
149C TYR 2.9 32.1 + - - -
156C ALA* 3.6 16.1 - - + +
157C TYR* 4.1 2.2 - - + -
191C VAL* 3.7 14.8 - - + -
193C GLU 3.3 15.0 - - - +
194C ASP* 2.8 28.7 + - - +
196C CYS* 3.1 18.0 - - - +
205C LYS* 1.3 72.3 + - - +
207C VAL* 1.3 62.4 + - - +
208C PHE* 3.6 28.9 - - + -
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Residues in contact with VAL 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C GLN* 4.0 15.9 - - + +
147C ILE 3.9 3.1 - - - +
148C THR* 3.8 27.6 - - + +
191C VAL* 3.4 6.8 - - - +
192C LEU* 2.7 60.4 + - + -
193C GLU* 3.0 18.1 + - + +
205C LYS* 4.5 19.1 - - - +
206C THR* 1.3 75.5 - - - +
208C PHE* 1.3 67.4 + - - +
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Residues in contact with PHE 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C GLN 4.5 0.2 - - - -
146C GLN* 3.0 9.5 - - - +
147C ILE* 2.9 58.3 + - + +
149C TYR* 3.9 7.6 - - + -
156C ALA* 3.7 10.3 - - + -
157C TYR* 4.5 2.2 - - + -
169C LEU* 3.5 40.8 - - + -
171C LEU* 4.3 7.4 - - + -
189C TYR* 3.6 48.7 - + + -
190C THR 3.4 3.1 - - - +
191C VAL* 4.2 9.9 - - + -
206C THR* 3.6 36.1 - - + -
207C VAL* 1.3 74.7 - - - +
209C GLU* 1.3 62.7 + - - +
223C ILE* 5.8 0.4 - - + -
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Residues in contact with GLU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C SER* 4.9 0.5 + - - -
145C GLN 3.2 15.3 - - - +
146C GLN* 3.1 30.8 + - + +
171C LEU* 6.1 0.9 - - - -
189C TYR* 3.4 4.3 - - - -
190C THR* 2.7 57.7 + - - +
192C LEU* 4.3 17.6 - - + +
208C PHE* 1.3 77.2 - - - +
210C TYR* 1.3 65.8 + - - +
211C ARG* 2.8 49.3 + - + +
220C ILE* 6.3 0.2 - - - -
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Residues in contact with TYR 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C SER* 3.3 4.7 - - - -
145C GLN 3.0 32.9 + - - +
171C LEU* 5.7 1.1 - - + -
179C PHE* 3.3 58.2 - + + -
186C LYS 2.6 29.0 + - - -
187C PHE* 4.0 3.0 - - - -
188C THR 3.7 26.7 - - - -
189C TYR* 4.2 4.5 - - + -
209C GLU* 1.3 75.8 - - - +
211C ARG* 1.3 68.7 + - - +
212C THR* 3.5 27.8 - - + -
217C ARG* 3.1 25.7 + - + -
218C LEU* 4.0 15.8 - - + +
220C ILE* 5.1 5.3 - - + +
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Residues in contact with ARG 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C GLU* 4.9 7.3 + - - -
142C ARG* 6.1 3.8 - - - +
143C ALA 3.6 3.6 - - - +
144C SER* 3.4 31.3 + - - -
146C GLN* 5.0 1.4 - - - +
209C GLU* 2.8 40.1 + - - -
210C TYR* 1.3 84.7 - - - +
212C THR* 1.3 64.7 + - - +
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Residues in contact with THR 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ARG* 3.2 6.9 - - - +
143C ALA 2.9 37.3 + - - +
210C TYR* 3.5 31.0 - - + +
211C ARG* 1.3 76.4 - - - +
213C ARG* 1.3 57.1 + - - +
214C LYS* 2.9 34.8 + - - +
215C ALA* 4.4 2.6 + - - +
217C ARG* 3.6 20.0 + - + -
218C LEU* 4.2 9.6 - - + -
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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