Contacts of the strand formed by residues 189 - 198 (chain A) 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 ILE 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLY 3.2 5.2 - - - +
138A ARG* 3.5 52.7 - - + +
187A GLY 3.5 0.4 + - - +
188A ASP* 1.3 70.5 - - - +
190A VAL* 1.3 62.9 + - - +
213A LEU* 3.8 0.5 - - - -
214A LEU* 2.8 35.1 + - + -
215A SER* 2.9 30.1 + - - +
351B TYR* 3.3 26.7 - - + +
546B GLY* 4.6 1.3 - - - +
547B LEU* 4.2 4.7 - - - -
548B PRO* 3.6 39.3 - - + -
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Residues in contact with VAL 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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135A ILE 4.1 0.2 - - - +
136A THR* 3.2 4.9 - - - -
137A GLY 2.9 28.1 + - - -
139A ILE* 3.7 34.1 - - + -
154A LEU* 3.9 12.6 - - + -
184A ILE* 4.5 13.5 - - + -
188A ASP* 4.3 12.1 - - + +
189A ILE* 1.3 79.3 - - - +
191A GLY* 1.3 63.1 + - - +
192A ILE* 4.3 13.8 - - + +
211A THR* 4.0 13.5 - - + -
212A ILE 3.3 15.5 - - - +
213A LEU* 4.1 8.3 - - + -
214A LEU* 3.7 5.2 - - - -
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Residues in contact with GLY 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.8 16.6 - - - -
135A ILE 3.6 5.2 - - - -
136A THR* 3.7 5.4 - - - -
190A VAL* 1.3 75.0 - - - +
192A ILE* 1.3 66.2 + - - +
211A THR* 3.6 1.2 - - - +
212A ILE* 3.0 33.4 + - - +
214A LEU* 3.3 20.9 - - - +
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Residues in contact with ILE 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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106A PHE* 3.4 3.4 - - - -
133A LEU 3.5 1.4 - - - +
134A ASN* 3.1 6.2 - - - -
135A ILE* 2.8 39.3 + - + +
139A ILE* 5.4 1.1 - - + -
154A LEU* 3.7 28.5 - - + -
163A VAL* 3.8 27.1 - - + -
190A VAL* 4.3 11.9 - - + -
191A GLY* 1.3 79.5 - - - +
193A VAL* 1.3 65.6 + - - +
206A ILE* 3.6 28.0 - - + -
208A PRO* 3.5 22.2 - - + -
210A GLU 3.7 3.1 - - - -
211A THR* 4.0 17.9 - - + +
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Residues in contact with VAL 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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106A PHE* 4.3 13.2 - - + -
132A ILE* 3.7 22.7 - - + -
133A LEU 3.5 2.7 - - - -
134A ASN* 3.8 20.6 - - - +
171A ASN* 6.4 0.2 - - - +
192A ILE* 1.3 73.2 - - - +
194A GLY* 1.3 54.1 + - - +
208A PRO* 3.3 1.9 - - - +
209A LYS* 2.5 38.3 + - + +
210A GLU* 3.0 45.3 + - + +
212A ILE* 5.0 3.6 - - + -
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Residues in contact with GLY 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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132A ILE* 4.3 5.3 - - - +
133A LEU* 2.9 39.5 + - - +
192A ILE* 3.9 3.4 + - - +
193A VAL* 1.3 76.7 - - - +
195A PHE* 1.3 61.2 + - - -
206A ILE* 4.1 8.2 - - - +
207A PHE 3.0 13.9 - - - -
208A PRO* 3.8 2.7 - - - -
209A LYS* 3.9 10.8 - - - -
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Residues in contact with PHE 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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127A HIS* 3.3 32.5 - + + -
128A LEU 3.0 28.3 - - - +
129A GLU* 3.5 30.1 - - + +
131A THR 3.5 13.0 - - - +
132A ILE* 4.5 1.8 - - + -
169A PHE* 3.6 41.7 - + + -
194A GLY* 1.3 75.4 - - - -
196A PRO* 1.3 65.0 - - - +
206A ILE* 4.3 2.2 - - - -
207A PHE* 2.9 61.5 + + + -
209A LYS* 4.7 13.7 - - + -
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Residues in contact with PRO 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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115A PHE* 3.4 28.0 - - + -
119A TYR* 3.4 45.1 - - + -
122A LEU* 4.9 1.1 - - - -
128A LEU* 3.1 31.9 + - + +
131A THR* 3.7 14.1 - - - +
133A LEU* 3.7 17.0 - - + -
195A PHE* 1.3 91.0 - - + +
197A GLY* 1.3 59.0 + - - +
205A SER 3.6 7.0 - - - +
206A ILE* 4.4 0.2 - - - -
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Residues in contact with GLY 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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122A LEU* 3.9 13.3 - - - +
126A GLU 3.3 14.8 - - - -
127A HIS* 4.3 1.1 - - - -
128A LEU 4.7 0.4 - - - -
196A PRO* 1.3 75.7 - - - +
198A LYS* 1.3 66.4 + - - -
204A LEU* 3.8 2.1 - - - +
205A SER* 2.6 31.9 + - - +
207A PHE* 3.6 11.1 - - - -
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Residues in contact with LYS 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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119A TYR 4.9 0.2 - - - +
120A LYS 3.8 17.7 + - - +
121A ASP* 5.4 0.2 - - - +
122A LEU* 3.1 49.7 + - + +
123A GLY 3.2 17.7 - - - +
124A ASN* 4.1 8.2 + - - +
125A GLY* 3.9 9.6 - - - +
126A GLU 3.2 8.0 + - - +
127A HIS* 4.6 1.9 + - - -
197A GLY* 1.3 78.8 - - - -
199A SER* 1.3 69.3 + - - +
202A GLY* 3.3 30.5 + - - -
203A GLU 3.5 5.6 - - - +
204A LEU* 4.0 17.3 - - + +
205A SER* 3.9 2.9 - - - -
207A PHE* 3.6 10.4 - - - -
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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