Contacts of the strand formed by residues 178 - 184 (chain A) in PDB entry 1FIB
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 PHE 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A PHE* 3.4 9.1 - - - -
169A ILE* 3.1 36.7 + - + +
171A PRO* 3.5 38.6 - - + -
174A ALA* 4.2 8.7 - - + -
176A GLN 3.7 12.1 - - - -
177A GLN* 1.3 73.7 - - - +
179A LEU* 1.3 65.5 + - - +
180A VAL* 3.6 26.9 - - + -
228A LEU* 4.6 0.4 - - + -
232A LYS* 3.9 53.2 - - + +
235A LEU* 4.8 6.5 - - + -
236A ILE* 4.0 13.2 - - + -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 3.6 42.8 - - + -
166A LEU* 3.6 38.1 - - + -
167A TYR 3.4 12.8 - - - +
168A PHE* 3.8 18.4 - - + -
178A PHE* 1.3 80.6 - - - +
180A VAL* 1.3 88.0 + - - +
218A LEU* 3.7 26.3 - - + +
228A LEU* 4.1 6.4 - - - +
232A LYS* 5.5 1.7 + - - -
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A CYS* 3.9 17.9 - - - -
166A LEU* 3.4 4.8 - - - -
167A TYR 2.9 38.8 + - - +
169A ILE* 3.8 35.2 - - + -
178A PHE* 3.6 28.3 - - + -
179A LEU* 1.3 86.9 - - - +
181A TYR* 1.3 59.8 + - - +
182A CYS* 3.8 2.6 + - - -
192A THR* 4.5 9.0 - - + -
193A VAL 5.2 1.3 - - - +
218A LEU* 4.6 4.3 - - - -
228A LEU* 4.1 20.4 - - + -
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Residues in contact with TYR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A CYS* 4.1 2.2 - - - -
164A SER* 3.8 14.0 - - - -
165A GLY* 3.5 16.4 - - - -
166A LEU* 3.8 9.6 - - + -
180A VAL* 1.3 73.2 - - - +
182A CYS* 1.3 73.9 + - - +
183A GLU* 4.5 13.1 - - + +
193A VAL* 3.2 47.1 + - + -
218A LEU* 4.3 15.5 - - + +
219A SER 3.3 28.3 - - - -
220A PRO 3.8 10.1 + - - -
221A THR 4.1 5.0 + - - -
222A GLY* 3.6 26.4 + - - -
226A PHE* 4.7 12.3 - + + -
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Residues in contact with CYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A CYS* 2.0 54.1 - - + -
156A ILE* 4.2 5.8 - - - -
164A SER* 3.2 6.2 - - - -
165A GLY 2.9 30.6 + - - +
167A TYR* 3.6 41.1 - - + -
180A VAL* 4.1 4.9 - - - -
181A TYR* 1.3 77.5 - - - +
183A GLU* 1.3 60.0 + - - +
184A ILE* 4.3 9.9 - - + -
191A TRP 3.4 0.2 - - - -
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A SER* 3.7 9.6 - - - +
181A TYR* 4.0 10.4 + - + +
182A CYS* 1.3 73.0 - - - +
184A ILE* 1.3 60.6 + - - +
185A ASP* 4.1 1.3 - - + -
189A ASN 3.5 1.7 - - - +
190A GLY* 3.5 1.2 - - - -
191A TRP* 2.8 53.5 + - + +
193A VAL* 3.8 15.3 - - + +
196A LYS* 5.7 1.9 + - - -
249A GLU* 4.6 0.5 - - - +
383A THR* 4.5 4.9 - - - +
385A LYS* 2.7 42.2 + - - +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A CYS 4.7 0.9 - - - +
156A ILE* 4.4 9.6 - - + -
157A ALA* 4.2 18.8 - - + +
161A ALA* 4.0 39.9 - - + +
162A LYS* 4.1 22.0 - - + +
163A GLN 3.9 20.4 - - - +
164A SER* 3.1 17.3 + - - -
167A TYR* 4.2 5.6 - - + +
182A CYS* 4.3 12.6 - - + -
183A GLU* 1.3 77.7 - - - +
185A ASP* 1.3 71.3 + - - +
188A GLY* 4.9 4.7 - - - -
189A ASN 3.3 9.9 - - - +
190A GLY* 4.3 6.1 - - - -
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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