Contacts of the strand formed by residues 188 - 198 (chain C) in PDB entry 4YCV
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 ASP 188 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C ARG* 2.6 29.9 + - - -
138C ARG* 3.4 0.7 - - - -
139C ILE* 2.9 30.1 + - - +
183C LYS 4.1 3.3 - - - +
184C ILE* 4.5 3.9 - - + -
185C ARG* 3.4 30.3 + - - +
186C ARG 4.5 0.7 - - - +
187C GLY* 1.3 78.4 - - - +
189C ILE* 1.3 63.0 + - - +
190C VAL* 3.6 13.1 + - + +
213C LEU* 5.1 10.0 - - + +
215C SER 4.0 1.3 - - - +
216C ALA* 4.0 6.7 - - - +
217C CYS* 2.5 36.4 + - - +
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Residues in contact with ILE 189 (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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136C THR* 5.7 1.8 - - - -
137C GLY* 3.5 13.2 - - - +
138C ARG* 3.3 47.3 - - + +
187C GLY 3.7 0.2 + - - -
188C ASP* 1.3 70.9 - - - +
190C VAL* 1.3 60.9 + - - +
213C LEU* 3.6 3.6 - - - +
214C LEU* 2.8 45.7 + - + -
215C SER* 2.8 41.1 + - - +
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Residues in contact with VAL 190 (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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136C THR* 3.3 5.4 - - - +
137C GLY 2.9 39.1 + - - +
139C ILE* 4.0 19.5 - - + -
154C LEU* 3.7 22.4 - - + -
184C ILE* 4.6 15.0 - - + -
188C ASP* 4.0 11.7 - - + +
189C ILE* 1.3 80.9 - - - +
191C GLY* 1.3 60.4 + - - +
192C ILE* 4.4 9.0 - - + -
211C THR* 4.2 13.9 - - + -
212C ILE 3.6 9.4 - - - +
213C LEU* 4.2 15.7 - - + -
214C LEU* 4.0 7.2 - - - +
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Residues in contact with GLY 191 (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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106C PHE* 3.6 22.4 - - - -
135C ILE 3.2 9.6 - - - -
136C THR* 3.7 7.4 - - - -
190C VAL* 1.3 74.6 - - - +
192C ILE* 1.3 65.6 + - - +
211C THR* 3.8 0.5 - - - +
212C ILE* 2.9 36.4 + - - +
214C LEU* 4.2 2.7 - - - +
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Residues in contact with ILE 192 (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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106C PHE* 3.3 5.1 - - - -
133C LEU 3.1 2.9 - - - +
134C ASN* 3.1 6.9 - - - -
135C ILE* 2.8 38.2 + - + +
139C ILE* 5.7 0.2 - - + -
154C LEU* 3.6 29.6 - - + -
163C VAL* 3.9 26.9 - - + -
190C VAL* 4.4 5.4 - - + -
191C GLY* 1.3 80.8 - - - +
193C VAL* 1.3 69.5 + - - +
206C ILE* 3.8 26.7 - - + -
208C PRO* 3.6 22.0 - - + -
210C GLU 3.8 2.7 - - - -
211C THR* 3.8 19.3 - - + +
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Residues in contact with VAL 193 (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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106C PHE* 4.6 8.7 - - + -
132C ILE* 3.6 25.4 - - + -
133C LEU 3.4 3.1 - - - +
134C ASN* 3.1 24.5 - - - +
192C ILE* 1.3 73.3 - - - +
194C GLY* 1.3 50.7 + - - +
208C PRO* 3.5 0.2 - - - +
209C LYS* 2.7 34.5 + - + +
210C GLU* 3.0 45.8 + - + +
212C ILE* 6.3 1.6 - - + -
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Residues in contact with GLY 194 (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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132C ILE* 3.6 7.2 - - - -
133C LEU* 2.8 35.1 + - - +
192C ILE* 3.7 2.4 + - - +
193C VAL* 1.3 77.4 - - - +
195C PHE* 1.3 62.4 + - - -
206C ILE* 3.7 9.0 - - - -
207C PHE 3.1 15.0 - - - -
208C PRO* 3.7 3.4 - - - -
209C LYS* 3.7 7.4 - - - -
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Residues in contact with PHE 195 (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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127C HIS* 4.0 22.9 - + + -
128C LEU 3.0 31.0 - - - +
129C GLU* 4.3 12.3 - - + -
131C THR 3.1 13.5 - - - +
132C ILE* 4.5 8.3 - - + -
169C PHE* 3.5 48.0 - + + -
194C GLY* 1.3 76.3 - - - -
196C PRO* 1.3 72.1 - - - +
206C ILE* 3.6 4.7 - - - +
207C PHE* 2.9 67.8 + + + -
208C PRO 5.7 0.2 - - - -
209C LYS* 5.5 4.5 - - + -
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Residues in contact with PRO 196 (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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115C PHE* 3.5 25.6 - - + -
119C TYR* 3.3 43.5 - - + +
122C LEU* 5.4 0.7 - - - -
128C LEU* 3.4 33.2 + - + +
131C THR* 3.5 16.8 - - + +
133C LEU* 4.0 15.5 - - + -
195C PHE* 1.3 93.8 - - + +
197C GLY* 1.3 57.5 + - - +
205C SER 3.7 6.5 - - - +
206C ILE* 4.0 0.6 - - - -
207C PHE* 4.1 0.9 - - - -
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Residues in contact with GLY 197 (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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122C LEU* 4.6 7.9 - - - -
126C GLU 3.2 14.6 - - - -
127C HIS* 4.7 0.4 - - - -
128C LEU* 6.3 0.2 - - - -
196C PRO* 1.3 76.1 - - - +
198C LYS* 1.3 58.4 + - - -
204C LEU* 4.1 9.8 - - - +
205C SER* 2.7 37.9 + - - +
207C PHE* 3.2 18.4 - - - -
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Residues in contact with LYS 198 (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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122C LEU* 4.9 10.4 - - + +
123C GLY 4.1 13.4 + - - +
124C ASN* 4.8 2.9 - - - -
125C GLY* 2.9 17.2 + - - +
126C GLU 3.0 16.8 + - - +
127C HIS* 4.5 0.3 - - - -
197C GLY* 1.3 75.2 - - - -
199C SER* 1.3 63.7 + - - +
203C GLU 3.4 27.1 - - - +
204C LEU* 4.0 8.6 - - + +
207C PHE* 4.3 4.6 - - - -
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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