Contacts of the strand formed by residues 199 - 209 (chain A) in PDB entry 1UKC
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 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A LYS* 3.9 5.5 + - - -
118A LEU 3.5 8.7 - - - -
120A VAL* 3.7 15.7 - - - -
151A VAL* 4.0 7.5 - - - +
194A ILE* 2.9 16.4 + - - -
195A GLU* 3.3 22.2 - - - +
197A PHE 3.3 2.6 + - - -
198A GLY* 1.3 82.6 - - - +
200A ASP* 1.3 59.5 + - - -
201A PRO* 3.5 3.3 - - - +
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Residues in contact with ASP 200 (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 LYS* 3.6 34.3 + - - +
118A LEU 2.8 18.4 + - - +
120A VAL* 3.7 5.5 - - - +
194A ILE* 4.3 2.2 - - - -
199A GLY* 1.3 70.6 - - - -
201A PRO* 1.3 61.2 - - - +
202A ASP* 2.9 28.2 + - - +
203A HIS* 2.8 56.9 + - + +
204A ILE* 3.9 0.5 - - - +
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Residues in contact with PRO 201 (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 LYS* 4.4 5.4 - - + -
191A LYS* 3.0 55.9 + - + +
194A ILE* 4.0 12.8 - - + -
195A GLU* 4.0 32.5 - - + +
199A GLY 3.5 10.0 - - - +
200A ASP* 1.3 88.1 - - - +
202A ASP* 1.3 65.4 + - - +
203A HIS 3.2 0.9 - - - -
204A ILE* 3.5 15.3 + - + +
229A GLY 4.5 0.9 - - - +
230A LEU 5.5 0.2 - - - -
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Residues in contact with ASP 202 (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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191A LYS* 3.2 21.9 + - - +
200A ASP* 2.9 15.0 + - - +
201A PRO* 1.3 84.3 - - - +
203A HIS* 1.3 60.4 + - - +
204A ILE 3.9 1.6 - - - -
232A ILE* 3.6 23.7 - - - +
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Residues in contact with HIS 203 (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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119A PRO* 3.7 20.5 - - + +
120A VAL 2.9 20.8 + - - +
200A ASP* 2.8 34.1 + - + +
202A ASP* 1.3 80.6 - - - +
204A ILE* 1.3 58.2 + - - +
205A VAL* 4.8 2.2 - - + +
232A ILE* 3.6 27.4 - - + +
481A VAL 3.2 25.7 + - - -
482A GLN 3.2 21.7 + - - -
483A THR* 4.8 1.2 + - - -
484A LEU* 4.6 9.6 - - + +
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Residues in contact with ILE 204 (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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120A VAL* 3.7 17.3 - - + -
122A LEU* 4.1 27.4 - - + -
187A LEU 5.2 0.9 - - - +
190A VAL* 3.8 20.9 - - + -
191A LYS* 4.1 17.3 - - + +
200A ASP 3.9 6.7 - - - +
201A PRO* 3.5 27.6 - - + +
202A ASP 3.9 1.6 - - - -
203A HIS* 1.3 78.0 - - - +
205A VAL* 1.3 71.7 + - - +
206A ILE* 4.4 1.1 - - + -
230A LEU 3.5 27.1 - - - +
231A PHE* 3.1 7.3 - - + +
232A ILE* 2.7 35.4 + - - +
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Residues in contact with VAL 205 (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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120A VAL 2.9 13.2 + - - +
121A TRP* 3.7 1.7 - - - -
122A LEU* 2.9 26.2 + - - +
203A HIS* 4.8 1.8 - - + -
204A ILE* 1.3 76.6 - - - +
206A ILE* 1.3 72.9 - - - +
207A HIS* 3.9 0.8 + - + -
232A ILE* 4.6 2.9 - - + -
233A GLY* 3.5 13.7 - - - +
235A ILE* 4.0 11.0 - - + -
480A PHE* 3.9 21.3 - - + -
481A VAL* 3.9 29.8 - - + +
484A LEU* 3.5 32.5 - - + -
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Residues in contact with ILE 206 (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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122A LEU* 3.4 31.0 - - + +
124A ILE* 4.6 7.2 - - + -
187A LEU* 4.3 10.5 - - + -
204A ILE* 4.1 2.4 + - + -
205A VAL* 1.3 76.2 - - - +
207A HIS* 1.3 53.8 + - - +
208A GLY 4.2 0.4 - - - -
216A VAL* 3.9 21.8 - - + +
219A HIS* 3.8 23.3 - - + -
230A LEU 5.2 0.2 - - - +
231A PHE* 3.7 50.5 - - + -
233A GLY 3.2 11.7 + - - +
234A ALA* 3.2 12.1 - - + -
235A ILE 2.7 31.5 + - - +
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Residues in contact with HIS 207 (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 TRP* 2.9 43.4 + + + +
122A LEU 2.8 8.2 + - - +
123A PHE* 3.3 16.0 - + + -
124A ILE* 2.7 32.0 + - - -
205A VAL 5.1 0.2 - - - +
206A ILE* 1.3 74.9 - - - +
208A GLY* 1.3 67.8 + - - +
216A VAL* 4.2 2.0 - - - -
235A ILE* 3.4 30.4 - - + +
237A GLU* 2.8 33.2 + - + +
447A ILE* 4.3 7.4 - - + -
448A PHE* 3.7 22.0 - + - -
477A PHE* 4.3 6.9 - + - -
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Residues in contact with GLY 208 (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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124A ILE* 3.4 6.7 - - - -
207A HIS* 1.3 75.9 - - - +
209A VAL* 1.3 57.7 + - - -
212A GLY 3.3 22.2 - - - -
213A ALA* 3.3 9.8 - - - +
216A VAL* 3.5 9.3 - - - +
235A ILE 2.9 9.1 + - - +
237A GLU* 2.9 28.9 + - - +
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Residues in contact with VAL 209 (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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123A PHE* 3.5 30.3 - - + -
124A ILE 3.1 8.4 + - - +
126A GLY* 3.4 5.1 - - - +
134A ASN* 3.7 22.7 - - - +
207A HIS 4.3 0.2 + - - -
208A GLY* 1.3 71.9 - - - -
210A SER* 1.3 64.7 + - - +
212A GLY* 2.7 23.9 + - - -
213A ALA 3.4 1.1 - - - +
237A GLU* 3.2 36.6 - - - +
441A THR* 3.3 34.1 - - + -
444A LEU* 4.3 6.3 - - + -
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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