Contacts of the strand formed by residues 191 - 200 (chain E) in PDB entry 1KGC
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 TYR 191 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E LEU* 5.8 2.4 - - - +
152E GLY 2.9 24.9 + - - -
153E PHE* 2.7 47.2 + - + +
154E TYR* 3.9 14.9 - + - -
155E PRO 4.3 0.4 - - - -
156E ASP* 3.5 47.1 + - + -
179E PRO* 3.7 17.7 - - + -
180E LEU 3.1 22.2 - - - +
181E LYS* 3.5 36.8 - - + -
182E GLU* 3.9 3.1 - - - -
187E ASN 5.7 1.0 + - - -
189E SER 3.6 14.8 + - - -
190E ARG* 1.3 76.0 - - - +
192E CYS* 1.3 61.3 + - - +
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Residues in contact with CYS 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D TYR* 5.9 1.3 - - + -
181D TRP* 3.8 28.0 - - + +
150E ALA 3.1 11.0 - - - +
151E THR* 4.0 6.5 - - + -
153E PHE* 4.0 2.0 - - - -
179E PRO* 3.3 2.3 - - - +
180E LEU* 2.7 40.8 + - + +
182E GLU* 3.7 20.0 - - + +
191E TYR* 1.3 75.1 - - - +
193E LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D TRP* 5.1 3.4 - - - -
148E CYS 3.8 0.3 - - - +
149E LEU* 3.5 3.2 - - - +
150E ALA* 2.7 40.3 + - + +
153E PHE* 4.0 14.4 - - + -
158E VAL* 4.0 24.2 - - + +
160E LEU* 4.3 20.5 - - + +
175E THR* 4.1 15.3 - - + -
176E ASP* 3.5 42.0 - - + +
178E GLN 4.0 0.2 - - - -
179E PRO* 3.9 24.0 - - + -
192E CYS* 1.3 74.7 - - - +
194E SER* 1.3 66.4 + - - +
215E VAL* 6.1 0.4 - - + -
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Residues in contact with SER 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D THR* 3.5 8.7 - - - +
179D VAL* 4.5 2.3 - - - +
181D TRP* 4.0 10.9 - - - -
147E VAL* 4.9 2.0 - - - -
148E CYS 3.2 5.6 - - - -
149E LEU* 3.5 23.8 - - - -
160E LEU* 4.8 0.4 - - - -
175E THR* 3.8 3.5 - - - +
176E ASP* 2.5 52.8 + - - +
193E LEU* 1.3 76.0 - - - +
195E SER* 1.3 62.9 + - - +
196E ARG* 3.0 19.3 + - - -
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Residues in contact with SER 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E VAL* 3.3 5.4 - - - +
148E CYS* 2.8 33.9 + - - +
160E LEU* 3.4 25.7 - - - +
162E TRP* 2.9 25.2 + - - -
173E VAL* 3.9 0.5 - - - +
174E SER 3.4 7.0 + - - -
175E THR* 2.7 26.7 + - - -
194E SER* 1.3 75.7 - - - +
196E ARG* 1.3 69.2 + - - +
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Residues in contact with ARG 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D LEU* 4.3 5.6 - - + -
161D THR* 5.0 2.6 + - - -
164D THR* 3.6 22.9 + - - +
166D LEU* 5.0 6.3 - - + -
177D SER* 3.6 23.3 + - - -
178D ALA* 6.0 0.9 - - - -
179D VAL* 3.4 25.0 - - - +
145E THR* 4.0 12.3 - - + -
146E LEU 3.3 5.2 - - - +
147E VAL* 4.0 19.0 - - + +
162E TRP* 4.1 2.9 - - - -
172E GLY 3.7 0.6 - - - +
173E VAL* 3.3 8.0 - - - +
174E SER* 2.9 63.4 + - - +
175E THR 3.9 0.2 - - - -
176E ASP* 2.9 28.4 + - - +
194E SER* 3.0 24.4 + - - -
195E SER* 1.3 84.0 + - - +
197E LEU* 1.3 60.2 + - - +
198E ARG 4.2 0.2 - - - -
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Residues in contact with LEU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E ALA 3.6 1.7 - - - +
145E THR* 3.5 1.9 - - - -
146E LEU* 2.8 40.2 + - + +
162E TRP* 3.6 45.1 - - + +
164E VAL* 4.2 13.5 - - + -
169E VAL* 4.2 9.2 - - + -
171E SER 4.3 4.3 - - - +
172E GLY 3.4 6.5 - - - +
173E VAL* 3.7 21.8 - - + -
196E ARG* 1.3 74.3 - - - +
198E ARG* 1.3 67.5 + - - +
199E VAL* 4.2 12.1 - - + -
211E PHE* 3.8 28.5 - - + -
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Residues in contact with ARG 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D THR* 3.9 9.7 + - - +
143D ASP* 2.7 41.8 + - - -
166D LEU* 3.8 20.4 - - + -
168D MET* 3.5 31.6 - - - +
173D PHE* 3.6 11.8 - - - -
175D SER* 3.2 20.3 + - - -
137E GLU* 2.9 27.5 + - - +
141E THR* 3.8 16.8 + - - +
143E LYS* 3.5 13.9 - - + +
144E ALA 3.4 7.6 - - - +
145E THR* 3.2 18.1 + - + +
171E SER 5.1 0.2 - - - +
172E GLY* 2.8 19.6 + - - +
196E ARG 4.2 0.4 - - - -
197E LEU* 1.3 74.6 - - - +
199E VAL* 1.3 72.8 + - - +
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Residues in contact with VAL 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D MET* 3.7 10.3 - - - +
143E LYS* 3.5 5.5 - - - +
144E ALA* 2.8 35.1 + - + +
146E LEU* 4.5 4.9 - - + -
164E VAL* 5.8 1.3 - - + -
197E LEU* 4.2 20.6 - - + -
198E ARG* 1.3 80.1 - - - +
200E SER* 1.3 70.8 + - - +
203E PHE* 4.1 24.0 - - + -
204E TRP* 4.1 21.1 - - + +
211E PHE* 4.2 13.5 - - + -
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Residues in contact with SER 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D MET* 4.0 3.6 - - - +
171D MET* 4.8 16.2 - - - -
142E GLN 3.9 7.4 - - - -
143E LYS* 4.4 5.2 - - - +
144E ALA 4.4 0.2 - - - -
199E VAL* 1.3 82.3 - - - +
201E ALA* 1.3 63.5 + - - +
202E THR* 3.2 12.8 + - - -
203E PHE* 3.1 27.6 + - - +
204E TRP* 3.2 10.0 + - - +
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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