Contacts of the strand formed by residues 180 - 188 (chain D) in PDB entry 3FFC
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 LYS 180 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D GLU* 3.2 39.4 + - - +
16D LYS* 6.1 2.2 - - - +
92D LEU* 3.6 21.1 - - + -
122D PRO* 4.3 15.0 - - + -
123D ASN* 5.6 2.0 - - - +
124D ILE* 3.4 25.6 - - + +
171D VAL* 4.8 1.8 - - + -
172D LEU 3.4 11.9 - - - +
173D ASP* 3.6 21.3 + - - +
174D MET* 5.8 0.2 - - - -
175D ARG* 5.7 2.0 - - - +
178D ASP* 3.7 17.1 + - - +
179D PHE* 1.3 88.9 - - - +
181D SER* 1.3 61.7 + - - +
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Residues in contact with SER 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ILE* 4.9 1.8 - - - -
148D THR* 3.7 0.2 + - - -
149D ASP* 3.8 7.6 + - - -
170D CYS 3.5 0.9 - - - +
171D VAL* 4.5 2.4 - - - +
172D LEU* 2.7 64.6 + - - +
174D MET* 6.1 0.6 - - - +
179D PHE* 3.7 22.2 - - - -
180D LYS* 1.3 74.3 - - - +
182D ASN* 1.3 70.7 + - - +
183D SER* 3.3 1.2 + - - -
211E ARG* 3.7 14.4 + - - -
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Residues in contact with ASN 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D PRO* 4.1 9.6 - - - +
124D ILE* 3.5 29.5 - - - +
148D THR* 3.1 4.7 + - - -
149D ASP* 3.0 27.5 + - - +
150D PHE* 3.6 40.2 + - + +
152D SER* 3.9 19.5 + - - +
169D LYS* 4.5 15.5 + - + +
170D CYS 3.6 4.8 + - - +
171D VAL* 3.5 24.2 - - - +
180D LYS 4.5 0.2 + - - -
181D SER* 1.3 70.2 + - - +
183D SER* 1.3 63.5 + - - +
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Residues in contact with SER 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LEU* 4.0 13.0 - - - -
147D PHE 3.7 5.6 - - - -
148D THR* 3.8 4.1 + - - -
150D PHE* 3.8 3.5 - - - -
168D ASP 3.6 0.5 - - - +
169D LYS* 3.4 4.7 - - - -
170D CYS 2.9 32.7 + - - -
172D LEU* 3.1 31.3 - - - +
181D SER* 3.3 2.9 + - - -
182D ASN* 1.3 78.5 + - - +
184D ALA* 1.3 60.7 + - - +
158E THR* 5.7 0.2 - - - +
209E ARG* 3.2 26.8 + - - -
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Residues in contact with ALA 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LEU* 3.3 5.7 - - - +
147D PHE* 2.8 47.4 + - + +
150D PHE* 4.3 1.3 - - + -
156D VAL* 4.0 35.7 - - + -
166D ILE* 5.5 0.2 - - + -
167D THR* 3.8 9.4 - - - +
168D ASP 4.4 0.4 - - - -
169D LYS 4.4 4.5 - - - +
183D SER* 1.3 77.0 - - - +
185D VAL* 1.3 64.9 + - - +
199D PHE* 4.6 2.2 - - + -
209E ARG* 4.0 2.0 - - - +
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Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D VAL* 3.8 21.5 - - + -
145D CYS 3.3 3.8 - - - +
146D LEU* 4.0 8.5 - - + -
166D ILE* 3.5 3.5 - - - +
167D THR* 2.8 45.6 + - + +
184D ALA* 1.3 79.0 - - - +
186D ALA* 1.3 64.9 + - - +
187D TRP* 3.6 24.5 - - + -
199D PHE* 4.3 2.2 - - - -
160E VAL* 4.1 16.8 - - + -
162E LEU* 4.4 2.2 - - + -
207E SER* 4.2 3.4 - - - +
209E ARG* 3.5 35.9 - - - +
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Residues in contact with ALA 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D VAL* 3.5 1.7 - - - -
145D CYS* 2.8 35.3 + - + +
165D TYR 3.2 11.9 - - - +
166D ILE* 3.8 15.5 - - + -
185D VAL* 1.3 76.0 - - - +
187D TRP* 1.3 65.0 + - - +
193D PHE* 4.3 15.7 - - + -
198D ALA* 4.7 2.2 - - + -
199D PHE* 3.5 24.9 - - + -
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Residues in contact with TRP 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LYS* 3.8 31.6 - - + +
143D SER 3.5 15.5 - - - +
144D VAL* 3.9 11.0 - - + -
164D VAL* 3.7 3.3 - - - +
165D TYR* 3.0 74.6 + + + +
167D THR* 3.6 32.3 - - + -
185D VAL* 3.6 18.2 - - + -
186D ALA* 1.3 76.7 - - - +
188D SER* 1.3 68.8 + - - +
193D PHE* 4.1 6.1 - - - -
162E LEU* 3.7 36.2 - - + +
164E THR* 5.0 0.6 - - + +
193E LEU* 4.4 7.2 - - + -
195E GLU* 4.7 1.6 + - - -
205E ALA* 3.6 30.1 - - + -
206E LEU 5.0 2.7 - - - -
207E SER* 4.2 4.5 - - - -
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Residues in contact with SER 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ASP 4.2 0.5 - - - +
142D LYS* 3.5 23.5 - - - +
143D SER* 3.5 11.6 + - - +
163D ASP 2.6 24.9 + - - -
164D VAL* 3.6 17.1 - - - +
165D TYR* 5.3 0.9 - - - -
187D TRP* 1.3 85.2 - - - +
189D ASN* 1.3 67.0 + - - +
190D LYS* 3.3 15.2 + - - +
193D PHE* 3.7 23.1 - - - -
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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