Contacts of the strand formed by residues 194 - 209 (chain A) in PDB entry 5A19
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 ALA 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ASP* 4.4 5.6 - - - +
190A GLN* 3.4 5.4 - - - +
191A ASP* 2.9 37.8 + - + +
192A ARG 3.2 2.6 + - - -
193A GLY* 1.3 80.2 - - - +
195A VAL* 1.3 62.5 + - - +
312A ARG* 3.4 49.4 - - + +
313A ARG* 4.4 5.8 - - - +
337A THR* 3.4 5.2 - - + +
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 4.0 11.7 - - + -
141A TYR* 5.3 0.2 - - - +
143A THR* 4.2 6.6 + - - +
144A ASP* 4.8 4.6 + - - +
145A GLU* 3.0 46.7 - - - +
188A TYR* 3.8 17.7 - - + -
189A MET 3.5 4.3 - - - +
190A GLN* 5.0 1.3 - - + -
194A ALA* 1.3 80.6 - - - +
196A LEU* 1.3 68.1 + - - +
274A TRP* 4.2 11.0 - - + -
313A ARG* 3.8 29.1 - - - +
408A PEG 3.9 18.4 - - - +
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP* 6.1 0.2 - - - +
145A GLU* 6.2 1.6 - - - -
188A TYR* 3.4 3.6 - - - -
189A MET* 2.8 65.8 + - + +
191A ASP* 3.7 30.1 - - + +
195A VAL* 1.3 81.1 - - - +
197A PRO* 1.4 72.1 - - + +
198A ILE 3.5 0.2 + - - -
312A ARG* 3.9 20.4 - - - +
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Residues in contact with PRO 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLU* 3.9 33.7 - - + +
152A LEU* 3.8 31.9 - - + -
186A VAL* 4.1 9.2 - - + -
187A GLN 4.0 2.2 - - - +
188A TYR* 3.6 20.4 - - + -
196A LEU* 1.4 87.1 - - + +
198A ILE* 1.3 62.2 + - - +
235A TYR* 3.8 22.3 + - + +
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Residues in contact with ILE 198 (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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17A THR* 4.0 19.1 - - + -
187A GLN* 2.9 24.8 + - + +
188A TYR 4.0 2.2 - - - -
189A MET* 3.6 42.6 - - + +
196A LEU* 3.9 9.0 - - + +
197A PRO* 1.3 74.8 - - - +
199A ARG* 1.3 77.1 - - + +
234A LYS 4.3 6.9 - - - +
235A TYR* 3.5 15.6 - - - -
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 3.5 7.0 - - - +
187A GLN* 3.0 59.4 + - + +
198A ILE* 1.3 87.5 - - + +
200A VAL* 1.3 73.7 + - - +
201A HIS* 3.7 29.7 - - - +
234A LYS 5.4 0.9 - - - +
235A TYR* 3.6 19.2 - - - +
237A ASP* 2.7 45.6 + - - +
239A ASP* 3.4 28.7 + - - +
240A THR* 3.4 3.6 - - - +
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 5.3 0.7 - - + -
156A LEU* 4.0 18.4 - - + -
184A VAL* 4.4 4.0 - - + -
185A THR 3.8 10.8 - - - +
186A VAL* 4.2 10.3 - - + +
199A ARG* 1.3 80.3 + - - +
201A HIS* 1.3 60.0 + - - +
202A THR 3.9 6.1 - - - +
203A ILE* 3.5 34.5 - - + -
231A VAL* 3.9 26.0 - - + -
235A TYR* 2.8 23.0 + - + +
236A LEU* 4.2 5.6 - - + -
240A THR* 3.0 30.0 + - + -
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Residues in contact with HIS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.6 45.5 - - + +
185A THR* 2.8 24.1 + - + +
187A GLN* 4.4 6.3 - - + +
199A ARG* 3.6 26.2 + - - +
200A VAL* 1.3 73.1 - - - +
202A THR* 1.3 85.3 + - - +
239A ASP 4.2 1.8 - - - +
240A THR* 3.7 2.6 - - - -
241A ILE* 2.9 44.8 + - + +
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Residues in contact with THR 202 (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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183A GLN 3.8 0.3 - - - +
184A VAL* 3.6 0.9 - - - -
185A THR* 2.8 45.2 + - - +
200A VAL* 3.8 1.0 - - - +
201A HIS* 1.3 105.5 + - - +
203A ILE* 1.3 74.5 + - - +
204A VAL* 4.3 6.7 - - + -
241A ILE* 3.3 20.8 - - + +
243A HIS* 3.7 28.3 - - + +
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Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.1 14.6 - - + -
183A GLN 3.3 6.1 - - - +
184A VAL* 4.7 8.3 - - + -
200A VAL* 3.5 29.2 - - + -
202A THR* 1.3 74.3 - - - +
204A VAL* 1.3 72.5 + - - +
205A ILE* 4.0 9.2 - - + -
227A ILE* 3.7 48.9 - - + -
231A VAL* 4.2 14.1 - - + -
236A LEU* 4.3 7.0 - - + -
240A THR* 4.8 1.3 - - + -
241A ILE 2.9 10.5 + - - +
242A TYR* 3.7 8.5 - - + -
243A HIS* 2.8 27.5 + - - +
244A LEU* 4.7 0.9 - - - +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LYS 5.5 0.9 - - - +
182A THR* 3.2 5.9 - - - -
183A GLN* 2.8 66.0 + - + +
202A THR* 4.7 5.8 - - + -
203A ILE* 1.3 76.2 - - - +
205A ILE* 1.3 73.4 + - - +
206A SER* 4.5 4.0 - - - +
243A HIS* 3.2 26.9 - - + +
246A PRO* 4.1 19.3 - - + -
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.5 6.5 - - + -
164A LEU* 4.1 17.3 - - + -
181A LYS 3.5 9.2 - - - +
182A THR* 4.3 9.4 - - + -
203A ILE* 4.0 7.9 - - + -
204A VAL* 1.3 80.3 - - - +
206A SER* 1.3 69.2 + - - +
207A VAL* 4.7 0.7 - - + -
222A LEU* 4.0 30.3 - - + +
226A VAL* 4.2 18.4 - - + -
227A ILE* 3.8 31.6 - - + -
243A HIS 3.0 7.9 + - - +
244A LEU* 4.0 14.1 - - + -
245A GLN* 3.0 26.5 + - - +
246A PRO* 3.6 3.2 - - - +
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Residues in contact with SER 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A SER* 3.3 2.6 - - - -
181A LYS* 2.8 49.1 + - - +
204A VAL* 4.5 4.8 - - - +
205A ILE* 1.3 74.9 - - - +
207A VAL* 1.3 62.4 + - - +
245A GLN* 3.4 7.1 - - - -
246A PRO* 3.5 22.3 - - - +
247A SER* 5.0 7.1 + - - -
250A PHE* 4.0 15.2 - - - -
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Residues in contact with VAL 207 (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 LEU* 4.3 12.3 - - + -
175A TRP* 4.3 5.4 - - + -
176A LEU* 3.4 34.8 - - + -
177A ARG 4.1 7.0 - - - +
179A ASP 3.6 11.0 - - - +
180A SER* 3.7 14.4 - - - -
205A ILE* 4.7 0.9 - - + -
206A SER* 1.3 75.7 - - - +
208A GLN* 1.3 67.9 + - - +
209A HIS* 3.6 2.4 - - - -
222A LEU* 4.2 20.6 - - + -
245A GLN* 2.8 45.0 + - - +
250A PHE* 3.2 11.2 - - - -
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Residues in contact with GLN 208 (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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92A TYR* 2.7 26.2 + - - -
97A LYS 3.1 25.1 + - - -
98A GLY* 5.3 0.2 - - - -
176A LEU* 3.9 2.4 - - - +
177A ARG* 3.0 47.0 + - + +
179A ASP* 2.9 31.1 + - + +
207A VAL* 1.3 79.8 - - - +
209A HIS* 1.3 62.2 + - - +
250A PHE* 3.3 23.7 - - + +
251A VAL 3.3 19.8 + - - +
253A GLY* 3.5 21.9 - - - +
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Residues in contact with HIS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TRP* 3.3 19.5 - - + +
177A ARG* 2.9 24.3 + - - -
207A VAL 3.6 2.5 - - - +
208A GLN* 1.3 76.7 - - - +
210A ASP* 1.3 80.6 + - - +
213A VAL* 3.9 6.2 - - + +
218A MET* 3.4 41.3 - - + +
245A GLN* 3.4 14.7 + - - -
248A GLY 4.7 0.2 + - - -
249A ARG* 3.6 31.0 - - + -
250A PHE* 3.0 36.3 + - + -
251A VAL* 3.5 21.0 - - + -
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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
------------------------------------------------------------
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