Contacts of the strand formed by residues 191 - 197 (chain A) in PDB entry 1F11
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 SER 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A LYS 3.8 1.0 + - - +
150A ILE* 3.4 5.2 - - - +
151A ASP* 2.7 55.7 + - - +
152A GLY 3.8 5.4 + - - -
190A ASN* 1.3 74.8 - - - +
192A TYR* 1.3 62.2 + - - +
193A THR* 5.1 6.2 + - - -
208A SER* 5.9 1.8 - - - -
209A PHE 3.6 4.9 - - - -
210A ASN* 3.7 16.2 - - - -
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Residues in contact with TYR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.9 6.2 - - - +
132A VAL* 4.5 14.6 - - + -
148A TRP* 5.1 2.7 - + + -
149A LYS 3.6 1.6 - - - -
150A ILE* 3.5 40.5 - - + +
179A LEU* 5.1 2.5 - - + -
181A LEU* 4.0 10.8 - - + +
185A GLU 3.9 0.9 + - - -
186A TYR* 2.7 54.8 + + - -
189A HIS* 3.5 24.0 - - + +
190A ASN 3.5 19.1 - - - -
191A SER* 1.3 72.0 - - - +
193A THR* 1.3 61.6 + - - +
208A SER* 3.2 3.8 - - - -
209A PHE* 3.1 62.8 + + + -
211A ARG* 4.0 3.1 - - + -
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Residues in contact with THR 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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117A ILE* 4.3 0.2 - - - -
147A LYS 3.9 0.3 - - - +
148A TRP* 3.4 12.0 - - - -
149A LYS* 2.8 53.2 + - + -
191A SER* 4.1 5.6 + - - -
192A TYR* 1.3 71.3 + - - +
194A CYS* 1.3 71.8 + - - +
195A GLU* 4.0 20.0 - - + +
206A VAL* 4.2 13.0 - - + -
207A LYS 3.4 9.4 - - - +
208A SER* 2.9 21.0 + - - +
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Residues in contact with CYS 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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115A VAL* 4.2 5.1 - - + +
117A ILE* 3.4 18.8 - - + +
134A CYS* 2.0 51.4 - - + -
136A LEU* 4.7 3.4 - - - -
146A VAL* 4.2 19.1 - - - -
147A LYS 3.6 3.8 - - - -
148A TRP* 4.0 8.1 - - + -
193A THR* 1.3 74.3 - - - +
195A GLU* 1.3 64.2 + - - +
205A ILE 4.1 0.7 - - - +
206A VAL* 3.6 0.7 - - - -
207A LYS* 2.8 30.9 + - - +
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Residues in contact with GLU 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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145A ASN 4.3 0.2 - - - -
146A VAL* 3.3 4.8 - - - -
147A LYS* 2.8 69.5 + - + +
149A LYS* 2.8 41.6 + - + +
193A THR* 4.0 4.8 - - + +
194A CYS* 1.3 76.9 - - - +
196A ALA* 1.3 59.9 + - - +
197A THR* 4.2 2.9 + - - +
204A PRO* 4.1 19.0 - - + +
205A ILE 3.3 4.3 - - - +
206A VAL* 3.1 33.0 - - + +
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Residues in contact with ALA 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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113A PRO* 4.4 9.9 - - + -
115A VAL* 4.6 6.2 - - + +
136A LEU* 3.5 32.1 - - + -
144A ILE* 4.3 11.4 - - + -
145A ASN 3.2 6.3 - - - +
194A CYS* 6.3 0.2 - - - -
195A GLU* 1.3 73.0 - - - +
197A THR* 1.3 62.7 + - - +
204A PRO* 3.4 8.2 - - - +
205A ILE* 2.9 36.7 + - + +
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Residues in contact with THR 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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144A ILE* 3.3 7.4 - - - +
145A ASN* 2.7 53.2 + - - +
147A LYS* 5.5 6.2 + - - +
195A GLU* 4.6 3.8 + - - +
196A ALA* 1.3 78.8 - - - +
198A HIS* 1.3 62.7 + - - +
199A LYS 3.6 4.5 + - - +
200A THR 4.2 8.5 - - - +
201A SER* 3.9 14.8 - - - +
202A THR* 5.3 5.4 - - - +
203A SER 5.8 0.2 - - - -
204A PRO* 4.5 17.6 - - + +
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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