Contacts of the strand formed by residues 179 - 187 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286B VAL* 4.0 24.5 - - + +
108C TYR* 4.3 2.0 - - - -
109C GLN* 3.7 25.8 - - + +
110C GLN* 3.8 22.9 - - + +
144C THR* 3.2 6.8 - - - -
145C ARG* 2.9 45.0 + - + +
147C LEU* 4.0 16.6 - - + +
169C SER* 4.1 11.7 - - - +
170C LEU* 3.8 28.5 - - + -
178C PRO* 1.3 74.5 - - - +
180C LEU* 1.3 63.5 + - - +
181C HIS* 5.9 0.4 - - - -
211C GLY* 6.5 0.2 - - - -
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B ARG* 4.7 2.9 + - - -
105C ILE* 3.3 32.5 - - + -
108C TYR* 3.9 18.1 - - + +
110C GLN* 2.8 42.0 + - - +
111C TYR* 3.9 7.4 - - + -
139C PRO* 5.3 0.2 - - + -
142C ILE* 3.7 23.8 - - + -
143C VAL 3.6 9.6 - - - +
144C THR* 4.1 7.4 - - + -
179C LEU* 1.3 72.9 - - - +
181C HIS* 1.3 58.7 + - - +
182C ALA 3.6 23.1 - - - +
183C SER* 5.3 4.0 - - - -
205C LEU* 4.6 4.7 - - + -
214C PRO* 3.8 29.3 - - + +
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Residues in contact with HIS 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ARG* 3.8 16.0 - - - +
286B VAL 4.9 2.7 - - - -
81C PHE* 4.2 6.1 - + - -
88C ARG* 3.6 16.7 + - - -
92C TRP* 3.4 36.6 - + + -
143C VAL* 2.7 38.1 + - - +
144C THR* 4.3 2.5 - - - +
145C ARG* 4.7 1.6 - - + +
179C LEU* 3.4 2.5 + - - +
180C LEU* 1.3 74.0 - - - +
182C ALA* 1.3 60.4 + - - +
214C PRO* 3.4 4.6 - - - +
215C HIS* 2.9 44.3 + - - -
284C LEU* 2.8 37.2 + - + +
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Residues in contact with ALA 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ILE* 3.3 7.6 - - - -
143C VAL* 3.0 42.0 + - + -
180C LEU* 3.6 10.7 - - - +
181C HIS* 1.3 81.5 - - - +
183C SER* 1.3 60.2 + - - +
184C ILE* 4.0 7.9 - - + -
214C PRO* 4.0 2.7 - - - +
215C HIS* 3.4 23.1 - - + +
284C LEU* 3.8 18.2 - - + -
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C PRO* 3.4 26.0 - - - +
141C ILE 3.8 4.3 - - - -
142C ILE* 4.9 0.4 - - - -
180C LEU* 5.3 3.1 - - - -
182C ALA* 1.3 72.5 - - - +
184C ILE* 1.3 63.7 + - - +
185C SER* 4.7 3.8 + - - -
201C GLU* 6.2 0.3 - - - +
205C LEU* 3.6 30.3 - - - +
214C PRO* 4.4 2.2 - - - +
215C HIS 2.8 11.0 + - - +
216C ILE* 3.6 6.5 - - - +
217C VAL* 3.0 26.9 + - - +
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Residues in contact with ILE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C CYS* 5.8 0.7 - - + -
77C VAL* 4.3 23.6 - - + -
140C ASP* 3.4 6.3 + - - +
141C ILE* 2.9 66.0 + - + +
143C VAL* 3.9 25.8 - - + -
182C ALA* 4.3 9.0 - - + -
183C SER* 1.3 76.3 + - - +
185C SER* 1.3 61.1 + - - +
186C CYS* 4.5 1.3 - - - -
217C VAL* 3.7 17.5 - - + -
219C VAL* 3.7 29.2 - - + -
280C LEU* 4.5 4.7 - - + -
284C LEU* 4.4 9.6 - - + -
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Residues in contact with SER 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C PRO* 6.5 0.2 - - - -
140C ASP* 3.7 8.7 - - - +
183C SER* 4.0 4.6 - - - -
184C ILE* 1.3 73.8 - - - +
186C CYS* 1.3 54.2 + - - +
187C LYS* 4.2 2.6 - - - -
198C ALA* 4.8 2.0 - - - -
201C GLU* 5.9 0.2 - - - -
217C VAL 2.9 15.9 + - - -
218C VAL* 3.2 20.4 - - - +
219C VAL* 2.7 32.7 + - - +
4003C ACY 2.7 40.1 + - - +
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Residues in contact with CYS 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLY 5.5 0.4 - - - +
69C PHE* 4.0 13.2 - - + -
70C GLU* 3.9 23.0 - - + +
73C CYS* 4.0 19.7 - - - -
140C ASP* 2.7 14.0 + - - +
141C ILE* 3.5 33.4 - - - -
184C ILE* 4.4 6.5 - - - -
185C SER* 1.3 76.6 - - - +
187C LYS* 1.3 65.6 + - - +
188C TRP 4.2 0.2 - - - -
219C VAL* 3.4 6.1 - - - -
7777C MG 2.2 31.5 - - - -
6K C 4.1 4.9 + - - +
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Residues in contact with LYS 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C PHE* 3.9 2.7 - - - -
185C SER* 4.2 3.8 - - - +
186C CYS* 1.3 78.3 - - - +
188C TRP* 1.3 61.9 + - - +
189C THR 3.2 12.6 - - - +
190C ILE* 4.1 17.5 - - + -
194C ARG* 3.9 8.3 + - - +
195C ALA* 3.6 27.4 - - + +
197C ASN* 2.8 29.3 + - - -
198C ALA* 4.0 12.6 - - - -
218C VAL* 4.6 9.9 - - + -
219C VAL 3.0 9.5 + - - +
220C THR* 2.7 42.5 + - - +
231C ILE* 5.4 2.5 - - + -
4003C ACY 2.9 23.0 + - - +
7777C MG 4.3 0.2 - - - -
5K C 3.7 8.7 + - - -
6K C 3.7 10.5 + - - +
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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