Contacts of the strand formed by residues 190 - 197 (chain A) in PDB entry 1FIC
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 GLY 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A CYS* 3.8 21.3 - - - +
154A GLN* 2.8 32.7 + - - +
157A ALA* 3.9 2.6 - - - +
183A GLU 3.2 6.1 - - - -
184A ILE* 4.0 9.4 - - - -
188A GLY 3.8 0.6 + - - -
189A ASN* 1.3 73.7 - - - +
191A TRP* 1.3 60.9 + - - -
192A THR* 3.9 1.2 + - - -
386A ILE 4.3 1.4 - - - +
387A ILE* 3.7 11.6 - - - +
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Residues in contact with TRP 191 (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 1.8 - - - -
182A CYS* 3.4 2.8 - - - -
183A GLU* 2.6 56.5 + - + +
185A ASP* 4.2 11.3 + - + +
189A ASN* 4.1 23.7 - - + +
190A GLY* 1.3 74.0 - - - -
192A THR* 1.3 61.2 + - - +
193A VAL 3.4 2.4 + - - -
245A ALA 4.6 1.3 - - - -
246A LEU 5.2 0.2 - - - -
247A ARG* 3.5 59.0 - - + -
385A LYS* 3.6 49.4 - - + +
386A ILE 3.7 10.5 - - - -
387A ILE* 3.4 45.5 - - + -
392A LEU* 4.0 11.7 - - + -
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Residues in contact with THR 192 (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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152A ASP* 3.9 8.7 - - - +
153A CYS* 3.0 34.2 + - - +
154A GLN 4.7 0.5 + - - -
169A ILE* 4.6 1.8 - - + -
180A VAL* 4.0 25.6 - - + -
190A GLY 3.9 0.8 + - - -
191A TRP* 1.3 70.8 - - - +
193A VAL* 1.3 64.1 + - - +
194A PHE* 3.8 2.8 + - + -
228A LEU* 5.0 1.6 - - + -
236A ILE* 3.9 28.5 - - + -
244A TYR* 5.8 0.7 - - - -
385A LYS* 3.3 1.6 - - - -
386A ILE* 3.0 45.6 + - + +
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Residues in contact with VAL 193 (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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181A TYR* 3.1 45.9 + - + +
183A GLU* 4.2 17.7 - - + +
191A TRP 3.9 7.9 - - - +
192A THR* 1.3 74.4 - - - +
194A PHE* 1.3 62.0 + - - +
195A GLN 3.4 21.5 - - - +
196A LYS* 4.8 4.7 - - + -
226A PHE* 3.5 27.3 - - + -
228A LEU* 4.3 9.4 - - - +
383A THR* 3.7 11.9 - - + -
384A MET 3.7 7.4 - - - +
385A LYS* 4.0 11.9 - - + -
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Residues in contact with PHE 194 (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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192A THR* 4.6 3.8 - - + -
193A VAL* 1.3 75.0 - - - +
195A GLN* 1.3 56.2 + - - +
226A PHE* 3.8 6.1 - - - -
227A TRP* 3.5 23.2 - + - -
228A LEU* 3.1 35.1 + - + -
233A ILE* 3.5 38.3 - - + +
236A ILE* 6.4 0.4 - - + -
246A LEU* 3.8 23.3 - - + -
265A PHE* 3.9 19.3 - + - -
335A TRP* 4.5 4.9 - + - -
384A MET* 2.8 45.3 + - + -
385A LYS* 4.6 1.3 - - - -
386A ILE* 3.7 34.3 - - + -
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Residues in contact with GLN 195 (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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193A VAL* 3.4 11.9 - - - +
194A PHE* 1.3 79.0 - - - +
196A LYS* 1.3 66.9 + - - +
197A ARG* 3.4 14.2 - - - +
204A PHE* 4.5 2.7 - - + -
226A PHE* 3.4 11.0 - - - +
227A TRP* 3.3 33.0 - - + -
344A LEU* 2.9 24.4 + - - +
345A ASN* 2.8 20.3 + - - +
382A THR* 3.0 23.2 + - - +
383A THR* 3.5 2.3 - - - -
384A MET* 3.2 45.0 + - + +
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Residues in contact with LYS 196 (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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181A TYR* 6.3 2.7 - - - -
183A GLU* 5.7 1.4 + - - -
193A VAL* 4.8 4.3 - - + -
195A GLN* 1.3 78.6 + - - +
197A ARG* 1.3 71.9 + - - +
198A LEU* 4.2 18.0 - - + +
222A GLY* 3.9 20.6 - - - +
224A THR 3.3 24.7 - - - +
225A GLU* 3.3 7.2 - - - +
226A PHE* 3.2 39.7 + - + +
381A LYS* 5.6 7.5 - - - +
382A THR 3.4 7.5 + - - +
383A THR* 2.5 35.7 + - + +
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Residues in contact with ARG 197 (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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195A GLN* 3.4 10.1 - - - +
196A LYS* 1.3 74.2 - - - +
198A LEU* 1.3 67.0 + - - +
200A GLY* 5.4 0.4 - - - -
202A VAL 4.6 4.9 + - - -
204A PHE* 3.2 52.2 - - - +
225A GLU* 3.1 15.4 + - - +
344A LEU 3.0 22.8 + - - +
345A ASN* 3.3 11.5 + - - +
346A GLY 2.9 29.7 + - - +
347A VAL* 4.5 0.4 - - - +
348A TYR* 3.8 26.8 - - + +
367A ILE* 3.6 21.1 - - + +
380A LYS 4.4 0.2 - - - -
381A LYS* 3.3 3.2 - - - +
382A THR* 3.0 45.3 + - - +
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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