Contacts of the strand formed by residues 184 - 193 (chain D) in PDB entry 1F11
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 LEU 184 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D THR* 3.9 31.6 - - + +
146D GLY* 4.0 25.4 - - - +
147D TYR 3.7 15.0 - - - +
148D PHE* 4.0 5.4 - - + -
178D LEU* 3.3 10.7 - - - +
179D GLN* 2.8 41.6 + - - +
180D SER* 5.0 4.9 - - - +
183D ASP* 1.3 87.9 - - - +
185D TYR* 1.3 60.0 + - - +
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Residues in contact with TYR 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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41D HIS* 5.5 6.6 - - - -
110D THR* 5.7 4.5 - - + +
146D GLY* 2.8 24.9 + - - -
147D TYR* 2.7 50.0 + + + +
148D PHE* 3.8 25.7 - + - -
149D PRO* 5.0 0.2 - - + -
150D GLU* 3.6 42.6 - - + +
176D ALA* 3.9 16.2 - - + -
177D VAL 3.3 12.6 - - - -
178D LEU* 3.2 32.6 - - + +
184D LEU* 1.3 72.8 - - - +
186D THR* 1.3 62.9 + - - +
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Residues in contact with THR 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C LEU* 5.0 4.3 - - + -
178C THR* 5.9 4.3 - - + +
143D LEU* 4.1 10.3 - - + -
144D VAL 3.6 5.4 - - - +
145D LYS* 3.4 24.6 - - + +
146D GLY 3.4 2.9 + - - -
147D TYR* 4.1 0.9 - - - -
175D PRO 4.3 0.9 - - - +
176D ALA* 4.1 0.9 - - - -
177D VAL* 2.8 47.0 + - + +
179D GLN* 2.9 39.0 + - - +
185D TYR* 1.3 76.6 + - - +
187D LEU* 1.3 69.6 + - - +
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Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C SER* 6.5 0.2 - - - -
143D LEU* 3.5 5.2 - - - +
144D VAL* 2.9 38.2 + - + +
147D TYR* 3.4 8.9 - - + +
150D GLU* 5.1 1.1 - - - +
152D VAL* 3.2 40.4 - - + +
154D VAL* 3.8 15.7 - - + -
173D THR* 3.7 23.1 - - + -
174D PHE* 3.5 22.9 - - - +
175D PRO 4.5 1.8 - - - -
176D ALA* 3.7 13.0 - - + +
186D THR* 1.3 76.3 - - - +
188D SER* 1.3 85.5 + - - +
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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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133C VAL* 5.2 3.1 - - - +
135C PHE* 3.8 18.4 - - - -
176C SER* 3.3 23.7 + - - -
178C THR* 5.0 2.8 + - - -
142D CYS 3.3 13.0 - - - -
143D LEU* 3.8 16.7 - - - +
144D VAL 4.5 0.2 - - - +
174D PHE* 3.0 36.0 + - - +
187D LEU* 1.3 85.4 - - - +
189D SER* 1.3 61.5 + - - +
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Residues in contact with SER 189 (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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135C PHE* 3.7 4.1 - - - -
141D GLY* 3.3 2.1 - - - -
142D CYS 2.8 33.9 + - - +
154D VAL* 3.7 27.5 - - - +
157D TRP* 2.9 23.1 + - - -
171D VAL* 3.8 1.9 - - - +
172D HIS 3.3 10.5 + - - -
173D THR* 3.5 20.5 + - - -
187D LEU* 4.4 0.6 - - - +
188D SER* 1.3 76.2 - - - +
190D SER* 1.3 64.8 + - - +
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Residues in contact with SER 190 (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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135C PHE* 3.4 34.5 - - - -
137C ASN* 3.6 13.0 + - - -
139D THR* 4.2 6.7 - - - -
140D LEU 3.2 8.5 - - - -
141D GLY* 4.1 0.2 - - - -
157D TRP* 3.7 3.3 + - - -
169D GLY 4.3 0.2 - - - -
171D VAL* 3.3 2.9 - - - -
172D HIS* 2.9 49.2 + - - +
174D PHE* 3.9 3.1 - - - -
189D SER* 1.3 78.2 + - - +
191D VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 191 (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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138D VAL 3.8 1.2 - - - +
139D THR* 3.5 1.9 - - - -
140D LEU* 2.8 38.9 + - + +
157D TRP* 3.6 46.4 - - + +
166D LEU* 4.7 11.0 - - + -
168D SER 4.2 8.5 - - - +
169D GLY 3.6 4.7 - - - -
171D VAL* 4.1 17.7 - - + -
190D SER* 1.3 76.6 - - - +
192D THR* 1.3 66.5 + - - +
193D VAL* 3.9 22.2 + - + +
206D VAL* 4.7 4.9 - - + -
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Residues in contact with THR 192 (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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137C ASN* 4.4 10.2 + - - -
137D MET* 4.0 35.6 - - + +
138D VAL 3.5 7.0 - - - +
139D THR* 3.2 21.0 + - - +
168D SER 4.2 10.0 - - - +
169D GLY* 3.4 18.6 + - - -
172D HIS* 5.6 0.5 - - - -
191D VAL* 1.3 75.5 - - - +
193D VAL* 1.3 66.7 + - - +
194D PRO* 4.7 0.5 - - - +
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Residues in contact with VAL 193 (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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137D MET* 4.2 4.5 - - - -
138D VAL* 2.6 54.9 + - + +
140D LEU* 4.5 16.4 - - + -
166D LEU* 4.5 21.5 - - + -
191D VAL* 4.0 24.2 - - + +
192D THR* 1.3 80.1 - - - +
194D PRO* 1.3 75.1 - - + +
199D PRO* 4.1 15.7 - - + -
200D ARG* 4.4 9.9 - - + +
206D VAL* 5.0 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