Contacts of the strand formed by residues 180 - 193 (chain A) in PDB entry 1F0C
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 THR 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ARG* 3.0 17.0 + - - -
147A PHE* 3.4 38.4 - - + +
178A LEU* 4.2 2.0 - - + +
179A ASP* 1.3 120.2 + - - +
181A CYS* 1.3 62.1 + - - +
182A LEU 4.0 12.1 - - - +
183A LEU* 4.6 2.7 - - + -
354A LEU* 3.7 33.6 - - + +
355A VAL 3.6 10.5 - - - +
356A ALA* 4.0 2.2 - - - +
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Residues in contact with CYS 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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120A GLY* 3.7 0.7 - - - -
121A ARG* 2.9 61.3 + - - +
124A ALA* 4.2 5.2 - - - -
126A PHE* 4.4 5.7 - - - -
147A PHE* 3.4 4.9 - - - -
179A ASP 3.7 1.0 + - - -
180A THR* 1.3 73.0 - - - +
182A LEU* 1.3 60.8 + - - +
321A MET* 5.8 0.7 - - - -
322A CYS* 3.3 31.6 - - - -
327A VAL* 3.9 7.0 - - + -
355A VAL* 2.6 19.2 + - + +
356A ALA* 4.5 2.0 - - - -
358A CYS* 3.3 12.8 - - - -
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Residues in contact with LEU 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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63A ILE* 5.6 1.6 - - + -
118A VAL* 3.3 24.7 - - + -
119A TYR 2.8 32.5 - - - +
120A GLY* 3.5 9.0 - - - -
126A PHE* 4.5 5.8 - - + -
130A PHE* 3.5 26.5 - - + -
142A PHE* 4.1 5.8 - - + -
147A PHE* 4.3 1.8 - - - -
180A THR* 3.9 2.6 - - - +
181A CYS* 1.3 82.1 - - + +
183A LEU* 1.3 65.0 + - - +
184A ALA* 4.2 2.7 - - + +
321A MET* 3.4 33.9 - - + -
353A ALA 3.8 0.7 - - - +
354A LEU* 3.7 2.1 - - - -
355A VAL* 2.8 49.6 + - + +
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Residues in contact with LEU 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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117A LYS 3.8 1.0 - - - +
118A VAL* 3.3 3.8 - - - +
119A TYR* 2.8 49.6 + - + +
147A PHE* 4.0 10.7 - - + -
157A ILE* 3.8 21.8 - - + -
173A LEU* 4.1 11.9 - - + -
178A LEU* 3.5 28.3 - - + -
180A THR* 4.6 1.3 - - + -
182A LEU* 1.3 77.0 - - - +
184A ALA* 1.3 59.3 + - - +
185A ILE* 3.9 10.1 - - + -
352A CYS* 3.8 14.4 - - - -
353A ALA 3.6 0.2 - - - -
354A LEU* 3.6 43.7 - - + -
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Residues in contact with ALA 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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60A VAL* 3.7 15.0 - - + +
63A ILE* 3.7 40.8 - - + -
64A LEU* 5.1 6.1 - - + -
117A LYS 3.6 4.7 - - - +
118A VAL* 4.5 4.7 - - + +
182A LEU* 4.2 3.5 - - + +
183A LEU* 1.3 71.0 - - - +
185A ILE* 1.3 60.8 + - - +
351A THR 3.7 0.9 - - - +
352A CYS* 3.4 3.5 - - - -
353A ALA* 3.1 33.7 + - + +
355A VAL* 6.3 0.9 - - + -
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Residues in contact with ILE 185 (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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60A VAL* 4.1 2.2 - - - -
63A ILE* 5.8 1.2 - - - +
115A MET* 4.7 3.4 - - + -
116A ASN* 3.3 6.9 - - - +
117A LYS* 2.8 41.5 + - + +
119A TYR* 4.5 13.7 - - + -
157A ILE* 3.5 32.5 - - + -
161A VAL* 4.0 13.9 - - + -
172A LEU* 3.5 26.7 - - + -
173A LEU* 4.7 2.0 - - + -
183A LEU* 4.6 8.5 - - + -
184A ALA* 1.3 80.8 - - - +
186A SER* 1.3 75.2 + - - +
187A ALA* 4.7 1.1 - - + +
351A THR 3.2 6.1 - - - +
352A CYS* 4.0 17.5 - - + -
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Residues in contact with SER 186 (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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56A SER* 2.7 38.9 + - - -
59A SER* 3.4 22.1 + - - -
60A VAL* 3.6 9.2 - - - -
114A SER* 5.9 0.2 - - - -
115A MET 3.5 5.6 - - - -
116A ASN* 3.6 4.1 + - - -
185A ILE* 1.3 79.0 - - - +
187A ALA* 1.3 65.1 + - - +
188A VAL* 4.3 2.3 - - - +
350A ALA* 2.9 7.0 - - - +
351A THR 2.8 30.0 + - - +
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Residues in contact with ALA 187 (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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114A SER* 3.2 0.7 - - - -
115A MET* 2.9 50.1 + - + +
161A VAL* 4.4 12.3 - - + -
164A PHE* 3.5 21.4 - - + -
165A THR* 4.4 3.6 - - + -
186A SER* 1.3 77.7 + - - +
188A VAL* 1.3 68.3 + - - +
349A ALA 3.3 8.1 - - - +
350A ALA* 4.3 8.5 - - + -
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Residues in contact with VAL 188 (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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53A SER* 3.5 22.0 - - - +
55A PRO* 5.4 1.6 - - + -
56A SER* 4.1 20.4 - - - +
112A PHE* 3.7 16.2 - - + -
113A LYS 3.2 8.5 - - - +
114A SER* 3.5 19.1 - - - -
164A PHE* 4.1 2.5 - - - -
165A THR* 4.0 3.7 - - - +
186A SER* 4.3 4.0 - - - +
187A ALA* 1.3 83.1 - - - +
189A TYR* 1.3 61.8 + - - +
348A ALA* 3.3 5.8 - - - +
349A ALA* 2.8 49.9 + - + +
384B PHE* 4.0 10.1 - - + -
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Residues in contact with TYR 189 (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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111A SER 3.6 2.5 - - - +
112A PHE* 3.5 6.7 - - - -
113A LYS* 2.8 64.2 + - + -
164A PHE* 3.8 10.5 - - + +
165A THR* 3.7 24.5 - - - -
166A GLU* 3.4 25.9 - - + +
168A LYS* 4.6 2.0 - - + -
188A VAL* 1.3 75.3 - - - +
190A PHE* 1.3 63.9 + - - +
191A LYS* 3.5 32.7 - - + +
346A GLU* 2.4 40.7 + - + -
347A ALA 3.4 9.2 - - - -
348A ALA* 4.1 3.1 - - + -
384B PHE* 4.9 0.4 - - - -
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Residues in contact with PHE 190 (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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111A SER* 3.2 30.1 - - - -
112A PHE* 4.1 1.8 - - + -
189A TYR* 1.3 82.0 - - - +
191A LYS* 1.3 63.9 + - - +
192A ALA* 3.8 16.4 - - + -
244A TYR* 3.8 20.0 - + - -
248A THR* 3.4 33.0 - - + -
345A THR* 3.8 31.4 - - + -
346A GLU* 3.4 2.9 - - - +
347A ALA* 2.7 41.0 + - + +
374B ILE* 4.0 17.0 - - + -
383B LEU* 4.4 15.3 - - + -
384B PHE* 3.6 22.2 - + + -
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ILE 5.0 1.0 - - - +
111A SER* 3.3 19.7 + - - +
189A TYR* 3.5 31.3 - - + +
190A PHE* 1.3 79.1 - - - +
192A ALA* 1.3 68.5 + - - +
193A LYS* 6.2 2.0 - - - -
344A TYR* 4.0 43.1 + - + -
345A THR 3.4 12.1 - - - +
346A GLU* 4.2 12.2 + - + +
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Residues in contact with ALA 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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111A SER* 3.7 17.5 - - - +
190A PHE* 3.8 18.8 - - + -
191A LYS* 1.3 80.0 - - - +
193A LYS* 1.3 63.9 + - - +
244A TYR* 3.5 22.6 - - + -
245A VAL* 4.4 4.0 - - + +
344A TYR* 3.0 5.1 - - - +
345A THR 3.0 30.8 + - - +
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Residues in contact with LYS 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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191A LYS* 6.2 2.2 - - - -
192A ALA* 1.3 75.8 - - - +
194A TRP* 1.3 62.0 + - - +
197A PRO* 6.2 1.1 - - + -
244A TYR* 3.3 5.4 - - - -
245A VAL* 2.8 46.8 + - + +
343A GLU* 3.4 44.6 + - - +
344A TYR* 3.7 8.1 - - + -
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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