Contacts of the strand formed by residues 198 - 208 (chain A) in PDB entry 3MGO
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 GLU 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A ALA* 3.7 2.4 - - - +
194A VAL* 3.3 34.1 + - + +
195A SER* 3.4 19.4 + - - +
196A ASP 3.5 0.4 - - - -
197A HIS* 1.3 90.1 - - + +
199A ALA* 1.3 63.8 + - - +
248A VAL* 3.6 25.9 - - + +
249A VAL 3.4 7.4 - - - +
250A PRO* 4.4 10.1 - - + +
251A SER* 3.9 6.8 + - - +
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Residues in contact with ALA 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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191A HIS* 3.4 39.0 - - + +
192A HIS 3.3 9.4 - - - +
193A ALA* 3.9 4.9 - - + -
194A VAL* 4.0 5.2 - - - +
198A GLU* 1.3 76.1 - - - +
200A THR* 1.3 63.7 + - - +
201A LEU 3.7 0.3 + - - -
247A VAL 3.7 0.2 - - - +
248A VAL* 3.6 3.4 - - - -
249A VAL* 2.8 37.5 + - + +
251A SER* 5.0 5.2 - - - +
254A GLU* 4.4 4.0 - - - +
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Residues in contact with THR 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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190A THR 3.4 2.3 - - - +
191A HIS* 3.3 6.8 - - - -
192A HIS* 2.7 40.2 + - - +
194A VAL* 3.0 22.5 - - - +
199A ALA* 1.3 71.8 - - - +
201A LEU* 1.3 65.4 + - - +
202A ARG* 3.9 31.6 - - - +
246A ALA* 4.1 16.4 - - + -
247A VAL 3.7 7.2 - - - +
248A VAL* 4.7 9.1 - - + +
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Residues in contact with LEU 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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189A MET* 4.3 3.8 - - - -
190A THR 3.6 11.0 - - - +
191A HIS* 3.4 32.8 - - + -
199A ALA 3.7 1.2 + - - +
200A THR* 1.3 72.1 - - - +
202A ARG* 1.3 60.3 + - - +
217A TRP* 3.8 25.0 - - + -
246A ALA* 3.2 1.7 - - - -
247A VAL* 2.9 50.4 + - + +
249A VAL* 3.8 22.4 - - + -
254A GLU* 4.2 19.5 - - + +
257A TYR* 4.5 1.3 - - + -
274A TRP* 3.9 34.8 - - + +
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Residues in contact with ARG 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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189A MET* 3.3 8.1 - - - -
190A THR* 2.9 52.7 + - - +
192A HIS* 4.8 5.9 + - - -
200A THR* 3.9 23.8 + - + +
201A LEU* 1.3 72.8 - - - +
203A CYS* 1.3 61.9 + - - +
204A TRP* 3.4 27.1 - - - +
217A TRP* 4.4 0.2 - - - -
229A GLU* 5.3 1.6 + - - -
244A TRP* 3.2 55.6 - - + -
245A ALA 3.7 2.2 - - - -
246A ALA* 4.0 5.3 - - + +
98B ASP* 3.0 31.0 + - - +
99B MET* 3.6 29.2 - - - +
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Residues in contact with CYS 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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188A HIS 3.8 4.0 - - - -
189A MET* 4.5 4.9 - - + -
202A ARG* 1.3 71.0 - - - +
204A TRP* 1.3 66.8 + - - +
215A LEU* 4.1 5.2 - - + +
217A TRP* 3.7 8.4 - - + +
244A TRP* 3.1 25.3 - - - -
245A ALA* 2.9 21.2 + - + +
259A CYS* 2.0 53.4 - - + -
261A VAL* 4.5 5.6 - - - -
272A LEU* 4.1 19.7 - - - -
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Residues in contact with TRP 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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186A LYS 4.2 0.9 - - - -
187A THR* 3.1 30.3 - - - +
188A HIS* 2.8 51.0 + + + +
190A THR* 3.6 16.6 + - + +
202A ARG* 3.4 37.4 - - + +
203A CYS* 1.3 75.9 - - - +
205A ALA* 1.3 59.4 + - - +
206A LEU* 3.7 31.4 - - + -
215A LEU* 5.0 1.3 - - - -
234A ARG* 3.5 18.8 - - - -
242A GLN* 4.9 1.3 - - + -
243A LYS 3.9 4.0 - - - -
244A TRP* 3.5 22.7 - + + -
261A VAL* 5.7 0.3 - - - +
97B ARG 4.9 3.8 - - - -
98B ASP* 3.4 28.4 + - - -
99B MET* 3.6 21.1 - - - -
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Residues in contact with ALA 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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185A PRO* 4.0 7.6 - - + -
186A LYS 3.6 3.1 - - - -
187A THR* 4.4 4.0 - - + -
203A CYS 4.2 0.2 + - - -
204A TRP* 1.3 74.5 - - - +
206A LEU* 1.3 63.6 + - - +
208A PHE* 3.3 23.7 - - + -
213A ILE* 3.9 18.4 - - + -
215A LEU* 4.0 15.0 - - + -
242A GLN* 3.4 2.6 - - - -
243A LYS* 3.0 33.8 + - + +
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Residues in contact with LEU 206 (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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185A PRO* 3.4 0.9 - - - +
186A LYS* 2.7 48.5 + - + +
188A HIS* 4.3 24.2 - - + +
204A TRP* 3.7 28.3 - - + -
205A ALA* 1.3 82.9 - - - +
207A SER* 1.3 73.4 + - - +
208A PHE* 3.2 4.7 + - - -
241A PHE 3.8 2.7 - - - -
242A GLN* 3.5 31.2 - - + +
12B ARG 6.2 0.2 - - - +
14B PRO* 4.4 24.5 - - + -
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Residues in contact with SER 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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183A ASP* 3.4 18.4 - - - +
184A ALA 4.0 4.7 - - - +
186A LYS* 4.2 20.5 + - - +
206A LEU* 1.3 80.2 - - - +
208A PHE* 1.3 59.0 + - - +
238A ASP* 5.2 2.6 + - - -
240A THR* 3.5 30.2 + - - +
241A PHE 3.3 6.7 + - - -
242A GLN* 4.9 2.2 - - - +
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Residues in contact with PHE 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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183A ASP 3.0 13.7 - - - +
185A PRO* 3.5 30.3 - - + -
205A ALA* 3.3 32.8 - - + -
207A SER* 1.3 78.3 - - - +
209A TYR* 1.3 64.3 + - - +
210A PRO 3.2 19.5 - - - -
211A ALA 3.3 22.7 - - - -
213A ILE* 3.9 20.2 - - + -
233A THR* 4.1 3.4 - - + -
240A THR* 3.6 3.1 - - - -
241A PHE* 3.0 66.9 + - + -
242A GLN* 3.7 11.4 - - - -
243A LYS* 4.1 0.9 - - + -
263A HIS* 3.5 12.6 - + + -
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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