Contacts of the strand formed by residues 198 - 213 (chain A) in PDB entry 2P02
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A LEU* 3.4 40.2 - - + +
189A LEU* 4.1 2.0 - - + -
190A ARG* 3.7 29.8 - - + +
195A LEU* 3.1 43.8 + - + +
196A PRO 3.8 2.1 - - - +
197A TRP* 1.3 104.5 - - + +
199A ARG* 1.3 76.1 + - - +
229A VAL* 3.7 29.8 - - + -
230A GLN 3.9 1.8 - - - -
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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
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114A TYR* 5.4 0.2 - - + -
118A SER* 5.0 7.5 + - - -
119A LYS* 3.7 48.0 - - - +
190A ARG* 3.6 9.9 + - - +
196A PRO 2.9 27.9 + - - -
197A TRP 3.5 9.0 + - - +
198A LEU* 1.3 86.1 + - - +
200A PRO* 1.3 73.8 - - + +
201A ASP 3.4 2.4 + - - -
202A SER* 5.4 0.2 - - - -
229A VAL* 3.7 15.4 - - - +
230A GLN* 2.9 41.7 + - + +
231A HIS 3.9 11.7 - - - +
232A ASP* 3.2 32.0 + - - +
273A VAL 5.8 0.2 - - - +
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Residues in contact with PRO 200 (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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48A GLY* 4.5 0.2 - - - -
49A GLU 4.2 4.3 + - - -
50A GLY* 3.1 25.2 + - - -
112A ILE* 3.7 24.2 - - + +
113A GLY 4.0 20.9 - - - +
114A TYR* 3.7 36.1 - - + -
119A LYS* 5.1 2.0 - - + -
190A ARG* 3.7 22.5 + - - +
199A ARG* 1.3 94.8 - - + +
201A ASP* 1.3 59.3 + - - +
202A SER* 3.5 6.5 + - - -
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Residues in contact with ASP 201 (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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2A SAM 2.6 38.3 + - - -
50A GLY 3.5 14.4 - - - +
51A HIS* 3.4 9.5 - - - +
52A PRO* 3.9 4.7 - - - +
114A TYR* 3.3 18.2 + - - +
199A ARG 3.4 1.0 + - - -
200A PRO* 1.3 76.4 - - - +
202A SER* 1.3 64.2 + - - +
229A VAL* 3.6 2.3 - - - +
230A GLN* 2.9 38.1 + - + +
272A PHE* 3.6 12.7 - - - -
275A GLY* 3.7 0.7 - - - -
276A GLY* 2.8 22.5 + - - +
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Residues in contact with SER 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SAM 4.8 0.2 - - - -
47A VAL* 3.4 3.5 - - - +
48A GLY* 2.9 33.2 + - - +
51A HIS* 4.0 3.7 - - - +
183A ASN* 2.7 27.0 + - - +
186A LEU* 3.7 23.0 - - - +
200A PRO 3.5 5.0 + - - -
201A ASP* 1.3 78.4 + - - +
203A LYS* 1.3 70.2 + - - +
228A SER 3.3 11.4 - - - -
229A VAL* 3.8 8.1 - - - -
272A PHE* 5.0 0.9 - - - -
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Residues in contact with LYS 203 (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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1A CL 3.2 27.1 - - - +
2A SAM 3.4 44.1 + - - +
45A GLU* 3.9 23.1 + - - +
46A SER 3.5 7.4 - - - +
47A VAL* 3.9 13.0 - - + -
51A HIS* 3.8 6.3 - - + -
183A ASN* 4.0 0.9 - - - -
202A SER* 1.3 80.3 - - - +
204A THR* 1.3 70.1 - - - +
226A VAL* 5.5 1.5 - - - +
227A ILE* 3.5 0.5 - - - +
228A SER* 2.9 41.8 + - - +
287A LYS* 4.9 1.7 - - - +
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Residues in contact with THR 204 (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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45A GLU* 3.2 7.8 - - - +
46A SER 2.9 27.1 + - - +
179A ALA* 2.8 28.7 + - - +
182A LEU* 3.7 28.9 - - + -
183A ASN* 3.0 25.2 + - - +
186A LEU* 4.5 2.2 - - + -
203A LYS* 1.3 82.2 - - - +
205A GLN* 1.3 62.5 + - - +
226A VAL* 3.2 9.9 - - - -
227A ILE* 4.2 17.3 - - + -
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Residues in contact with GLN 205 (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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43A THR* 3.4 33.4 - - + +
44A SER 3.4 12.6 - - - +
45A GLU* 4.1 17.6 - - + +
179A ALA* 4.8 0.4 - - - -
204A THR* 1.3 77.0 - - - +
206A VAL* 1.3 64.6 + - - +
207A THR* 4.3 3.1 + - - +
224A THR* 3.9 0.7 - - - +
225A ILE* 3.3 5.0 - - - +
226A VAL* 2.8 59.2 + - + +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE 3.8 1.7 - - - +
43A THR* 3.3 2.6 - - - -
44A SER 2.9 31.9 + - - -
175A THR* 3.7 18.8 - - - +
178A LEU* 4.2 17.0 - - + -
179A ALA* 3.8 24.2 - - - +
182A LEU* 3.9 21.8 - - + -
205A GLN* 1.3 79.0 - - - +
207A THR* 1.3 65.0 + - - +
208A VAL* 4.0 23.3 - - + -
222A VAL* 4.3 12.6 - - + -
224A THR 3.6 2.2 - - - -
225A ILE* 4.6 6.1 - - + -
253A VAL* 6.0 0.7 - - + -
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Residues in contact with THR 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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41A LEU* 4.0 24.0 - - + -
42A PHE 3.3 7.0 - - - +
43A THR* 2.8 29.2 + - - +
205A GLN* 5.0 3.3 + - - +
206A VAL* 1.3 71.6 - - - +
208A VAL* 1.3 58.2 + - - +
222A VAL* 3.7 4.7 - - - +
223A HIS* 2.8 49.7 + - + +
224A THR* 2.9 30.5 + - - +
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Residues in contact with VAL 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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41A LEU* 3.4 6.4 - - - -
42A PHE 2.9 30.1 + - - -
174A LEU* 4.5 11.7 - - + -
175A THR* 3.6 20.6 - - + +
178A LEU* 4.8 1.1 - - + -
206A VAL* 4.0 14.8 - - + -
207A THR* 1.3 77.2 - - - +
209A GLN* 1.3 74.9 + - - +
210A TYR* 3.5 30.8 - - + -
219A PRO* 4.0 17.7 - - + -
221A ARG 3.4 9.2 - - - +
222A VAL* 4.2 13.5 - - + -
257A TYR* 6.5 0.2 - - + -
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Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 3.4 31.1 + - - +
40A PHE 3.4 9.9 - - - +
41A LEU* 3.8 19.3 - - + +
207A THR 4.4 0.2 + - - -
208A VAL* 1.3 73.9 - - - +
210A TYR* 1.3 55.1 + - - +
220A ILE* 2.8 52.6 + - + +
221A ARG* 2.9 47.6 + - + +
223A HIS* 4.5 4.5 - - + +
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Residues in contact with TYR 210 (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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39A THR* 3.1 8.7 - - - -
40A PHE* 2.8 63.9 + + + -
42A PHE* 4.0 2.7 - - + -
167A GLU* 2.7 28.8 + - - -
174A LEU* 3.7 8.3 + - - +
175A THR* 3.6 18.4 + - + +
208A VAL* 3.5 35.2 - - + -
209A GLN* 1.3 72.1 - - - +
211A MET* 1.3 60.5 + - - +
217A VAL* 3.7 22.2 - - + -
218A LEU 3.3 21.5 - - - -
219A PRO* 3.7 14.4 - - + -
220A ILE* 3.7 4.9 - - - -
296A TRP* 3.5 25.4 - + - -
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Residues in contact with MET 211 (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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38A GLY* 3.6 26.2 - - - +
39A THR* 3.7 17.7 - - + -
40A PHE* 4.4 2.5 - - - -
210A TYR* 1.3 73.2 - - - +
212A GLN* 1.3 75.7 + - - +
217A VAL* 3.6 3.8 - - - +
218A LEU* 2.8 51.8 + - + +
220A ILE* 3.8 16.0 - - + +
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Residues in contact with GLN 212 (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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38A GLY* 3.0 35.5 + - - +
40A PHE* 3.7 26.1 - - + +
211A MET* 1.3 88.6 - - - +
213A ASP* 1.3 59.5 + - - +
214A ARG 4.1 1.8 - - - +
215A GLY 5.8 1.6 - - - +
216A ALA 3.9 5.8 - - - +
217A VAL* 5.7 1.1 - - + -
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Residues in contact with ASP 213 (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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212A GLN* 1.3 75.3 - - - +
214A ARG* 1.3 72.9 + - - +
215A GLY 3.2 1.3 - - - +
216A ALA* 2.9 30.0 + - - +
218A LEU* 3.7 34.6 - - + +
334A ARG* 3.0 32.5 + - - -
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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