Contacts of the strand formed by residues 188 - 195 (chain A) in PDB entry 4F8Q
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 GLY 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASN* 3.6 23.8 + - - +
181A MET* 4.7 0.2 - - - -
187A GLU* 1.3 75.4 - - - +
189A VAL* 1.3 67.2 + - - +
206A ILE 3.5 10.5 - - - -
207A SER* 3.7 9.6 - - - -
208A ILE 4.7 0.2 - - - -
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Residues in contact with VAL 189 (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 LEU* 4.0 12.3 - - + -
150A TRP* 4.0 22.2 - - + -
151A SER 3.4 7.9 - - - +
152A ASN* 4.0 15.5 - - - +
158A ILE* 4.1 13.7 - - + -
179A VAL* 5.8 1.1 - - + -
181A MET* 4.0 27.6 - - + -
187A GLU* 6.1 0.7 - - + -
188A GLY* 1.3 78.6 - - - +
190A SER* 1.3 65.2 + - - +
205A SER* 3.6 1.3 - - - -
206A ILE* 2.8 55.0 + - + +
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Residues in contact with SER 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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149A GLN 3.8 0.3 - - - +
150A TRP* 3.3 10.6 - - - -
151A SER* 2.9 43.6 + - - -
152A ASN* 5.4 4.9 + - - -
189A VAL* 1.3 78.8 - - - +
191A CYS* 1.3 60.2 + - - +
192A ILE* 3.8 11.8 + - - -
203A THR* 4.5 5.4 - - - -
204A ALA 3.3 8.7 - - - -
205A SER* 3.1 20.2 + - - -
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Residues in contact with CYS 191 (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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121A LEU* 3.1 12.5 - - + +
123A VAL* 4.9 1.6 - - + -
137A CYS* 2.0 55.9 - - + -
148A ILE* 4.0 19.5 - - - -
149A GLN 3.7 4.5 - - - -
150A TRP* 4.1 16.4 - - + -
190A SER* 1.3 71.2 - - - +
192A ILE* 1.3 62.8 + - - +
193A ILE* 4.4 0.2 - - - -
203A THR* 3.3 1.9 - - - -
204A ALA* 2.8 40.9 + - + +
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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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147A GLN 3.7 1.6 - - - +
148A ILE* 3.5 2.3 - - - +
149A GLN* 2.9 54.0 + - + +
151A SER* 3.1 31.6 - - - +
190A SER* 4.3 13.9 - - - +
191A CYS* 1.3 75.5 - - - +
193A ILE* 1.3 67.3 + - - +
194A ARG* 4.5 2.6 - - + +
201A GLU* 3.2 37.9 - - + +
202A LYS 3.6 2.0 - - - -
203A THR* 3.9 16.8 - - + +
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Residues in contact with ILE 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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121A LEU* 3.8 20.2 - - + -
137A CYS* 4.7 0.4 - - - -
139A SER* 3.4 32.1 - - - +
142A TRP* 3.3 35.1 - - + +
146A PRO* 3.6 23.6 - - + -
147A GLN 3.5 5.6 - - - +
148A ILE* 3.5 35.0 - - + -
175A VAL* 4.2 4.7 - - + -
191A CYS* 4.4 0.4 - - - -
192A ILE* 1.3 76.4 - - - +
194A ARG* 1.3 60.6 + - - +
201A GLU* 3.1 2.5 - - - -
202A LYS 2.8 37.1 + - - +
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Residues in contact with ARG 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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142A TRP* 5.2 1.1 - - - -
146A PRO* 5.4 0.7 - - - -
147A GLN* 2.9 63.8 + - + +
149A GLN* 5.2 5.8 - - - +
192A ILE* 4.0 3.3 - - + -
193A ILE* 1.3 74.3 - - - +
195A ASN* 1.3 67.1 + - - +
196A SER* 4.0 12.7 + - - +
199A GLY* 3.6 33.8 + - - -
200A LEU 3.8 5.8 - - - +
201A GLU* 3.0 49.4 + - + +
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Residues in contact with ASN 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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115A ALA* 3.8 12.7 - - - +
116A ALA 5.2 4.6 + - - +
117A LEU* 6.0 0.4 - - - +
142A TRP* 4.8 13.0 - - + -
143A TYR 4.4 6.2 + - - +
144A PRO* 4.9 13.6 - - + +
145A GLN 6.0 0.7 - - - +
146A PRO* 5.5 6.5 - - + -
147A GLN 5.5 0.2 - - - +
193A ILE 4.3 0.6 + - - -
194A ARG* 1.3 72.6 - - - +
196A SER* 1.3 61.8 + - - +
197A LEU* 3.4 6.3 + - + +
198A LEU* 3.2 31.0 - - - +
199A GLY 3.0 17.8 + - - -
200A LEU* 2.7 47.8 + - - +
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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