Contacts of the strand formed by residues 179 - 187 (chain D) in PDB entry 1FIU
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 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A VAL* 4.0 23.3 - - + +
108D TYR* 4.3 1.8 - - - -
109D GLN* 3.9 27.4 - - + +
110D GLN* 3.7 23.3 - - + +
144D THR* 3.2 7.1 - - - -
145D ARG* 2.9 45.0 + - + +
147D LEU* 4.1 12.1 - - + -
169D SER* 4.2 13.2 - - - +
170D LEU* 3.7 29.6 - - + -
178D PRO* 1.3 75.8 - - - +
180D LEU* 1.3 63.2 + - - +
181D HIS* 5.2 0.4 - - - +
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Residues in contact with LEU 180 (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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212A ARG* 4.8 2.1 + - - -
105D ILE* 4.3 17.3 - - + -
108D TYR* 3.9 21.7 - - + +
110D GLN* 2.9 39.8 + - - +
111D TYR* 3.8 20.0 - - + -
139D PRO* 5.4 0.4 - - + -
142D ILE* 3.7 22.9 - - + -
143D VAL 3.7 15.7 - - - +
144D THR* 4.2 7.0 - - + -
179D LEU* 1.3 72.1 - - - +
181D HIS* 1.3 59.8 + - - +
182D ALA 3.7 15.7 - - - +
183D SER* 5.3 4.7 - - - -
205D LEU* 4.5 6.7 - - + -
214D PRO* 3.6 28.4 - - + +
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Residues in contact with HIS 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ARG* 3.7 10.0 + - - +
286A VAL 4.9 2.2 + - - -
81D PHE* 4.1 6.2 - + - -
88D ARG* 3.5 25.6 + - - -
92D TRP* 3.4 37.1 - + + -
143D VAL* 2.7 38.5 + - + +
144D THR* 4.3 2.5 - - - +
145D ARG* 4.8 1.6 - - + +
179D LEU 3.5 2.2 + - - +
180D LEU* 1.3 74.2 - - - +
182D ALA* 1.3 59.5 + - + +
214D PRO* 3.4 4.3 - - - +
215D HIS* 2.8 46.4 + + - -
284D LEU* 2.8 34.9 + - + -
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Residues in contact with ALA 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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142D ILE* 3.3 7.1 - - - -
143D VAL* 3.1 42.4 + - + -
180D LEU* 3.7 11.3 - - - +
181D HIS* 1.3 81.2 - - + +
183D SER* 1.3 60.4 + - - +
184D ILE* 4.0 8.1 - - + -
214D PRO* 4.0 2.9 - - - +
215D HIS* 3.4 22.4 - - + +
217D VAL* 5.9 0.2 - - + -
284D LEU* 3.8 18.4 - - + -
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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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139D PRO* 3.3 27.7 - - - +
141D ILE 3.8 3.8 - - - -
142D ILE* 5.0 0.2 - - - -
180D LEU* 5.3 2.5 - - - -
182D ALA* 1.3 73.6 - - - +
184D ILE* 1.3 61.0 + - - +
185D SER* 4.4 9.4 + - - -
201D GLU* 6.2 0.3 - - - +
205D LEU* 3.6 30.2 - - - +
214D PRO* 4.5 2.2 - - - +
215D HIS 2.8 13.5 + - - +
216D ILE* 4.6 6.7 - - - +
217D VAL* 3.1 26.7 + - - +
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Residues in contact with ILE 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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73D CYS* 5.6 0.4 - - + -
77D VAL* 4.2 24.2 - - + -
140D ASP* 3.4 6.1 + - - +
141D ILE* 2.9 66.0 + - + +
143D VAL* 4.0 24.2 - - + -
182D ALA* 4.4 9.0 - - + -
183D SER* 1.3 77.9 + - - +
185D SER* 1.3 63.2 + - - +
186D CYS* 4.4 2.0 - - - -
217D VAL* 3.7 16.4 - - + -
219D VAL* 3.8 28.7 - - + -
280D LEU* 4.5 4.7 - - + -
284D LEU* 4.4 9.0 - - + -
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Residues in contact with SER 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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139D PRO* 5.6 1.4 - - - +
140D ASP* 3.7 7.9 + - - +
183D SER* 4.0 8.7 + - - -
184D ILE* 1.3 73.9 - - - +
186D CYS* 1.3 57.9 + - - +
198D ALA* 4.6 3.9 + - - +
201D GLU* 4.9 4.5 + - - +
216D ILE* 6.0 1.7 - - - +
217D VAL 3.0 15.2 + - - -
218D VAL* 3.2 17.4 - - - +
219D VAL* 2.7 32.6 + - - +
5004D ACY 3.6 33.5 + - - +
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Residues in contact with CYS 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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66D GLY 5.5 0.2 - - - +
69D PHE* 3.9 14.8 - - + -
70D GLU* 3.9 26.4 - - + +
73D CYS* 4.0 15.9 - - - -
140D ASP* 2.8 14.0 + - - +
141D ILE* 3.6 33.2 - - - -
184D ILE* 4.4 6.7 - - - -
185D SER* 1.3 77.3 - - - +
187D LYS* 1.3 65.9 + - - +
188D TRP 4.2 0.2 - - - -
219D VAL* 3.4 5.6 - - - -
9999D MG 2.2 31.0 - - - -
6L C 4.2 4.9 + - - +
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Residues in contact with LYS 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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69D PHE* 3.7 2.6 - - - -
186D CYS* 1.3 78.4 - - - +
188D TRP* 1.3 62.2 + - - +
189D THR 3.3 12.6 - - - +
190D ILE* 4.1 14.1 - - + -
194D ARG* 3.6 11.6 + - - +
195D ALA* 3.6 30.3 - - + +
197D ASN* 2.7 29.1 + - - -
198D ALA* 4.1 7.0 - - - -
218D VAL* 4.6 13.0 - - + -
219D VAL 2.9 10.5 + - - +
220D THR* 2.8 41.6 + - - +
231D ILE* 5.6 2.2 - - + -
5004D ACY 3.0 25.4 + - - +
9999D MG 4.3 0.2 - - - -
5L C 3.7 10.7 + - - -
6L C 3.6 11.3 + - - +
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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