Contacts of the strand formed by residues 191 - 197 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C LYS 3.8 0.5 - - - +
150C ILE* 3.3 5.4 - - - +
151C ASP* 2.7 56.2 + - - +
152C GLY 3.8 5.2 + - - -
190C ASN* 1.3 75.9 - - - +
192C TYR* 1.3 62.4 + - - +
193C THR* 4.1 4.8 + - - -
208C SER* 5.9 2.7 - - - -
209C PHE 3.6 4.3 - - - -
210C ASN* 3.7 16.8 - - - -
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Residues in contact with TYR 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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117C ILE* 3.9 6.1 - - - +
132C VAL* 4.5 16.2 - - + -
148C TRP* 5.0 3.4 - + + -
149C LYS 3.5 2.5 - - - -
150C ILE* 3.5 42.0 - - + -
179C LEU* 5.0 2.2 - - + -
181C LEU* 3.9 11.4 - - + -
185C GLU 4.0 0.7 + - - -
186C TYR* 2.4 53.2 + + - -
189C HIS* 3.3 22.8 - - + +
190C ASN 3.5 19.1 - - - -
191C SER* 1.3 70.3 - - - +
193C THR* 1.3 61.2 + - - +
208C SER* 3.2 4.7 - - - -
209C PHE* 3.0 63.5 + + + -
211C ARG* 3.9 3.4 - - + -
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Residues in contact with THR 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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117C ILE* 4.4 0.4 - - - -
148C TRP* 3.3 12.1 - - - -
149C LYS* 2.8 53.5 + - + -
191C SER* 4.1 5.1 + - - -
192C TYR* 1.3 74.3 + - - +
194C CYS* 1.3 72.2 + - - +
195C GLU* 4.0 19.7 - - + +
206C VAL* 4.4 11.7 - - + -
207C LYS 3.5 8.7 - - - +
208C SER* 3.0 20.5 + - - +
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Residues in contact with CYS 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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115C VAL* 4.1 6.1 - - + +
117C ILE* 3.5 17.5 - - + +
134C CYS* 2.0 51.4 - - + -
136C LEU* 4.7 3.4 - - - -
146C VAL* 4.2 18.8 - - - -
147C LYS 3.6 3.8 - - - -
148C TRP* 4.0 8.7 - - + -
193C THR* 1.3 74.3 - - - +
195C GLU* 1.3 61.9 + - - +
196C ALA 5.6 0.2 - - - -
205C ILE 4.0 0.3 - - - +
206C VAL* 3.6 1.2 - - - -
207C LYS* 2.8 30.2 + - - +
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Residues in contact with GLU 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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146C VAL* 3.4 3.5 - - - -
147C LYS* 2.8 70.1 + - + +
149C LYS* 2.8 41.8 + - + +
193C THR* 4.0 4.9 - - + +
194C CYS* 1.3 76.7 - - - +
196C ALA* 1.3 61.1 + - - +
197C THR* 4.2 3.5 + - - +
204C PRO* 4.0 19.9 - - + +
205C ILE 3.2 4.0 - - - +
206C VAL* 3.2 34.1 - - + +
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Residues in contact with ALA 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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113C PRO* 4.6 6.1 - - + -
115C VAL* 4.6 11.8 - - + +
136C LEU* 3.5 31.4 - - + -
144C ILE* 4.4 10.1 - - + -
145C ASN 3.4 6.7 - - - +
194C CYS* 5.6 0.4 - - - -
195C GLU* 1.3 72.5 - - - +
197C THR* 1.3 61.9 + - - +
204C PRO* 3.5 8.5 - - - +
205C ILE* 2.9 37.8 + - + +
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Residues in contact with THR 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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144C ILE* 3.2 8.3 - - - +
145C ASN* 2.7 52.9 + - - +
147C LYS* 5.4 6.1 + - - +
195C GLU* 4.4 5.6 + - - +
196C ALA* 1.3 77.8 - - - +
198C HIS* 1.3 60.5 + - - +
199C LYS 3.6 5.5 + - - +
200C THR 4.0 5.2 - - - +
201C SER 3.6 22.4 - - - +
202C THR* 5.4 1.8 - - - -
203C SER 5.8 0.7 - - - -
204C PRO* 4.5 13.6 - - + +
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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