Contacts of the strand formed by residues 191 - 198 (chain F) in PDB entry 3SRF
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 PHE 191 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141F ILE 3.3 10.1 - - - +
142F THR* 5.0 7.6 - - + +
143F LEU* 6.0 0.4 - - - -
164F CYS* 3.6 3.8 - - - -
186F GLN* 5.1 6.3 - - + -
187F LYS 4.0 15.0 - - - -
188F GLY* 3.2 45.8 + - - -
189F ALA 3.6 4.6 - - - -
190F ASP* 1.3 95.2 - - - +
192F LEU* 1.3 77.2 + - - +
193F VAL* 4.7 13.5 - - + -
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Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F LEU 3.9 0.5 - - - +
140F LYS* 3.4 2.6 - - - +
141F ILE* 2.6 59.8 + - + +
163F ILE* 4.2 20.4 - - + -
164F CYS* 3.7 17.9 - - - -
167F VAL* 3.9 29.4 - - + -
173F ILE* 4.1 22.4 - - + -
184F VAL* 4.3 8.3 - - + -
186F GLN 3.8 7.2 - - - +
187F LYS* 4.0 18.2 - - + -
191F PHE* 1.3 82.7 - - - +
193F VAL* 1.3 64.2 + - - +
194F THR* 4.0 5.4 - - + -
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Residues in contact with VAL 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F THR* 3.9 18.2 - - - +
139F LEU 4.1 2.2 - - - -
140F LYS* 4.0 20.0 - - + -
184F VAL* 3.8 0.5 - - - -
185F LYS* 2.8 34.7 + - + -
186F GLN* 2.9 48.9 + - + +
191F PHE* 4.7 13.4 - - + -
192F LEU* 1.3 75.9 - - - +
194F THR* 1.3 58.0 + - - +
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Residues in contact with THR 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F THR* 3.4 9.9 + - - -
139F LEU* 2.7 48.1 + - - +
141F ILE* 3.9 22.6 - - + +
173F ILE* 4.2 5.2 - - + -
182F LEU* 3.9 26.6 - - + +
183F GLN 3.4 7.9 - - - -
184F VAL* 3.8 30.1 - - + +
185F LYS* 4.1 4.5 - - - -
192F LEU* 4.6 4.7 - - + -
193F VAL* 1.3 78.5 - - - +
195F GLU* 1.3 60.4 + - - +
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Residues in contact with GLU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F GLY* 3.3 39.3 - - - +
137F ALA 3.5 3.1 - - - +
138F THR* 4.6 1.6 - - - +
182F LEU* 3.4 3.6 - - - -
183F GLN* 2.8 32.1 + - - +
185F LYS* 3.8 29.2 + - + +
194F THR* 1.3 74.9 - - - +
196F VAL* 1.3 71.6 + - - +
197F GLU* 3.3 19.6 + - - +
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Residues in contact with VAL 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F LEU* 3.7 33.7 - - + -
134F LYS 3.2 24.9 - - - +
136F GLY* 2.9 29.8 + - - -
137F ALA* 2.7 27.3 + - + +
138F THR 4.8 0.4 - - - +
139F LEU* 4.4 9.9 - - + -
180F ILE* 4.9 0.4 - - + -
181F SER 3.7 7.0 - - - +
182F LEU* 4.0 8.3 - - + -
195F GLU* 1.3 73.1 - - - +
197F GLU* 1.3 60.9 + - - +
198F ASN 3.7 25.6 - - - +
199F GLY* 4.0 7.9 - - - +
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Residues in contact with GLU 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F LYS* 3.3 27.9 + - - +
172F LYS* 4.4 13.4 + - - +
181F SER* 2.8 34.3 + - - +
182F LEU 4.4 0.2 - - - -
183F GLN* 3.0 47.9 - - + +
195F GLU* 3.9 21.6 - - - +
196F VAL* 1.3 72.7 - - - +
198F ASN* 1.3 61.7 + - - +
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Residues in contact with ASN 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337E PRO* 4.7 13.6 - - + +
338E ARG* 6.3 0.4 - - - +
369E TYR* 6.5 0.7 - - + -
135F LYS* 3.9 17.0 - - - +
179F LEU 2.9 21.7 - - - +
180F ILE* 3.7 2.4 - - - +
181F SER* 3.5 32.5 + - - -
196F VAL* 3.7 9.3 - - - +
197F GLU* 1.3 80.6 - - - +
199F GLY* 1.3 64.2 + - - +
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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