Contacts of the strand formed by residues 198 - 210 (chain A) in PDB entry 3NUM
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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189A PHE* 4.1 21.0 - - + +
190A ARG 3.1 19.1 - - - +
191A LYS* 3.9 28.3 - - - +
196A LYS 3.3 8.0 + - - +
197A ARG* 1.3 76.6 - - - +
199A VAL* 1.3 69.0 + - - +
227A ARG* 3.3 51.0 + - - +
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Residues in contact with VAL 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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189A PHE* 3.4 6.7 - - - -
190A ARG* 2.8 34.7 + - + +
192A LEU* 3.7 42.8 - - + -
197A ARG* 4.4 4.0 - - + +
198A GLU* 1.3 81.8 - - - +
200A PRO* 1.4 77.8 - - + +
201A VAL* 3.3 4.2 + - + +
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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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187A GLU* 3.4 30.3 - - + +
188A LEU 3.4 9.2 - - - +
189A PHE* 3.3 21.7 - - + -
199A VAL* 1.4 90.3 - - + +
201A VAL* 1.3 62.7 + - - +
202A ALA 5.1 0.9 - - - +
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Residues in contact with VAL 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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188A LEU* 2.5 35.1 + - + +
190A ARG* 4.3 22.0 - - + -
199A VAL* 3.3 6.0 + - + +
200A PRO* 1.3 76.4 - - - +
202A ALA* 1.3 64.2 + - + +
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Residues in contact with ALA 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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187A GLU* 3.4 5.8 - - - +
188A LEU* 2.5 53.1 + - + +
200A PRO* 5.1 1.5 - - - -
201A VAL* 1.3 86.8 - - + +
203A SER* 1.3 61.7 + - - +
220A HIS 4.6 10.5 - - - +
221A VAL* 4.5 7.6 - - - +
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Residues in contact with SER 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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185A HIS* 2.8 34.1 + - - -
186A ILE 3.5 6.1 - - - -
187A GLU* 4.2 8.7 - - - +
202A ALA* 1.3 75.8 - - - +
204A GLY* 1.3 56.5 + - - +
221A VAL* 4.5 10.9 - - - +
325A TYR* 5.4 3.7 - - - +
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Residues in contact with GLY 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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185A HIS* 3.0 14.7 + - - -
186A ILE 2.8 33.4 + - - -
203A SER* 1.3 77.7 + - - +
205A SER* 1.3 60.2 + - - -
221A VAL* 3.8 17.7 - - - +
284A SER 5.3 0.4 - - - -
325A TYR 4.9 8.7 - - - -
328A ALA* 4.3 5.2 - - - -
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Residues in contact with SER 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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184A VAL 3.2 11.7 - - - -
186A ILE* 3.8 6.6 - - - +
204A GLY* 1.3 77.0 + - - -
206A GLY* 1.3 59.0 + - - +
217A THR* 3.0 22.2 + - - -
221A VAL* 4.0 0.5 - - - +
283A GLY* 3.5 17.2 - - - -
284A SER 3.2 20.3 + - - -
325A TYR 4.6 0.9 + - - -
326A GLY 3.4 11.6 + - - -
328A ALA 3.2 19.1 + - - -
329A GLY* 3.2 9.3 - - - -
330A GLY* 3.7 8.7 - - - -
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Residues in contact with GLY 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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183A VAL* 3.4 8.7 - - - +
184A VAL* 2.8 37.8 + - - +
186A ILE* 3.9 13.0 - - - +
205A SER* 1.3 75.1 - - - +
207A PHE* 1.3 62.4 + - - +
215A ILE* 4.5 0.2 - - - -
216A VAL 3.3 14.4 - - - -
329A GLY 3.9 6.3 - - - -
330A GLY* 4.7 1.3 - - - -
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Residues in contact with PHE 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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182A ALA 3.1 16.2 - - - +
183A VAL* 4.3 2.2 - - - -
184A VAL* 4.2 2.7 - - - -
206A GLY* 1.3 75.5 - - - +
208A ILE* 1.3 65.7 + - - +
209A VAL* 3.5 26.2 - - + -
215A ILE* 3.1 7.2 - - - +
216A VAL* 2.8 44.8 + - + -
265A LEU* 3.9 16.2 - - + -
267A LEU* 4.7 3.4 - - + -
329A GLY 4.3 0.2 - - - -
330A GLY 4.2 1.1 - - - -
331A PRO* 3.5 30.7 - - + -
339A VAL* 3.7 32.5 - - + -
342A ILE* 2.9 38.6 - - + -
360A ILE* 4.7 3.8 - - + -
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Residues in contact with ILE 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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181A PRO 4.1 5.2 - - - +
182A ALA* 3.0 24.1 + - - +
184A VAL* 3.9 18.4 - - + -
207A PHE* 1.3 79.9 - - - +
209A VAL* 1.3 61.8 + - - +
210A SER 3.2 28.5 - - - +
213A GLY* 4.4 1.3 - - - -
214A LEU 3.3 11.9 - - - +
215A ILE* 3.9 14.1 - - + -
232A LEU* 5.7 4.3 - - + -
262A LEU* 4.4 22.0 - - + -
263A PRO* 3.4 34.5 - - + +
264A VAL* 4.6 0.2 - - - -
265A LEU* 3.1 24.1 + - - +
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Residues in contact with VAL 209 (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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207A PHE* 3.5 29.8 + - + +
208A ILE* 1.3 77.4 - - - +
210A SER* 1.3 60.1 + - - +
214A LEU* 2.9 31.6 + - + +
216A VAL* 4.1 24.7 - - + -
253A LEU* 4.8 0.2 - - + -
264A VAL* 3.8 14.9 - - - +
265A LEU 4.3 9.2 - - - +
267A LEU* 4.7 9.6 - - + -
360A ILE* 5.9 0.2 - - + -
364A LEU* 4.6 18.2 - - + -
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Residues in contact with SER 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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208A ILE* 3.2 15.8 - - - +
209A VAL* 1.3 81.6 - - - +
211A GLU* 1.3 55.9 + - - +
212A ASP* 2.4 28.0 + - - -
213A GLY 2.9 17.5 + - - -
214A LEU* 2.8 33.8 + - - +
264A VAL* 3.6 12.3 - - - +
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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