Contacts of the strand formed by residues 190 - 197 (chain F) in PDB entry 4KKA
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 190 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148F LYS 3.4 3.5 - - - +
150F ASP* 2.6 51.4 + - - -
151F GLY 4.1 1.5 + - - -
189F ASN* 1.3 74.3 - - - +
191F TYR* 1.3 58.0 + - - +
192F THR* 4.2 11.5 - - - +
207F SER* 5.1 3.5 - - - -
208F PHE 3.6 1.8 + - - -
209F ASN* 2.8 24.0 + - - -
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Residues in contact with TYR 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F ILE* 4.9 1.0 - - - +
131F VAL* 4.6 13.2 - - + -
147F TRP* 5.1 4.3 - + + -
148F LYS 3.8 2.2 - - - -
149F ILE* 3.4 47.5 - - + +
178F LEU* 4.9 5.2 - - + -
180F LEU* 4.1 9.4 - - + +
184F GLU 4.1 0.5 + - - -
185F TYR* 2.4 61.4 + + - -
188F HIS* 3.7 7.5 - - + +
189F ASN 3.7 13.2 - - - -
190F SER* 1.3 72.2 - - - +
192F THR* 1.3 63.6 + - - +
207F SER* 3.3 4.3 - - - -
208F PHE* 2.9 68.6 + + + +
210F ARG* 3.9 11.7 - - - -
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Residues in contact with THR 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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116F ILE* 4.6 0.4 - - - -
147F TRP* 3.4 13.9 - - - -
148F LYS* 3.0 57.5 + - + +
151F GLY* 5.2 5.2 - - - +
190F SER* 4.2 12.1 - - - +
191F TYR* 1.3 78.0 - - - +
193F CYS* 1.3 62.1 + - - +
194F GLU* 4.3 9.4 + - - +
205F VAL* 5.4 4.0 - - + -
206F LYS 3.4 4.5 - - - -
207F SER* 3.0 23.6 - - - +
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Residues in contact with CYS 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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114F VAL* 4.4 2.7 - - - +
116F ILE* 3.5 14.6 - - + -
133F CYS* 2.0 53.6 - - - -
135F LEU* 4.3 2.7 - - - -
145F VAL* 3.8 24.5 - - - -
146F LYS 4.3 1.3 - - - -
147F TRP* 4.1 10.1 - - + -
192F THR* 1.3 74.4 - - - +
194F GLU* 1.3 60.2 + - - +
195F ALA 4.0 0.4 + - - -
204F ILE 3.7 0.9 - - - +
205F VAL* 3.1 6.6 - - - +
206F LYS 2.8 31.1 + - - +
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Residues in contact with GLU 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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144F ASN 3.4 2.3 - - - +
145F VAL* 3.1 6.9 - - - -
146F LYS* 2.8 60.7 + - + +
148F LYS* 3.6 35.3 + - + +
192F THR* 4.3 11.9 + - - +
193F CYS* 1.3 75.5 - - - +
195F ALA* 1.3 60.3 + - - +
196F THR* 4.8 1.7 + - - +
203F PRO* 4.3 16.3 - - + +
204F ILE 3.5 2.0 - - - -
205F VAL* 3.4 30.3 - - + +
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Residues in contact with ALA 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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112F PRO* 5.1 3.4 - - + -
114F VAL* 3.7 21.8 - - + -
135F LEU* 3.6 29.2 - - + -
143F ILE* 4.7 4.9 - - + -
144F ASN 3.4 4.3 - - - -
145F VAL* 4.4 1.8 - - - +
193F CYS 4.0 0.6 + - - -
194F GLU* 1.3 73.8 - - - +
196F THR* 1.3 61.3 + - - +
197F HIS* 4.4 0.7 + - - -
203F PRO* 3.2 4.0 - - - +
204F ILE* 2.7 48.1 + - + +
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Residues in contact with THR 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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143F ILE* 3.3 6.4 - - - +
144F ASN* 2.7 50.6 + - + +
194F GLU* 4.8 1.7 + - - +
195F ALA* 1.3 75.1 - - - +
197F HIS* 1.3 67.8 + - - +
200F SER 5.1 4.7 - - - +
201F THR 5.6 4.3 - - - +
203F PRO* 3.5 24.1 - - + +
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Residues in contact with HIS 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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110F ALA 3.2 15.5 - - - -
112F PRO* 3.5 22.0 - - + +
138F PHE* 3.8 6.4 - + + +
139F TYR 3.2 25.5 - - - -
140F PRO* 3.1 28.4 + - + +
142F ASP 3.3 26.2 - - - -
143F ILE* 4.0 14.6 - - + -
195F ALA 4.4 0.6 + - - -
196F THR* 1.3 79.8 - - - +
198F LYS* 1.3 67.0 + - + +
199F THR* 2.5 38.2 + - + +
200F SER* 2.8 24.5 + - - +
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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