Contacts of the strand formed by residues 205 - 218 (chain A) in PDB entry 4MDR
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A VAL* 4.2 13.2 - - + -
198A LEU 3.7 8.1 - - - +
199A ILE* 4.2 9.9 - - + +
203A GLY 3.8 2.6 + - - +
204A SER* 1.3 74.9 - - - +
206A LEU* 1.3 62.8 + - - +
207A LYS 3.2 31.0 - - - +
208A VAL* 4.1 22.4 - - + -
289A ASP* 4.0 21.8 - - - +
290A LEU* 5.9 1.1 - - + +
294A LEU* 4.4 26.9 - - + -
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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
----------------------------------------------------------
198A LEU* 2.8 40.8 + - + +
200A ALA* 4.0 25.8 - - + +
204A SER* 4.6 4.3 - - - +
205A LEU* 1.3 80.9 - - - +
207A LYS* 1.3 71.5 + - + +
452A ARG* 3.6 31.0 - - - +
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Residues in contact with LYS 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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197A VAL* 3.2 3.1 - - - -
198A LEU* 2.9 51.5 + - + +
205A LEU* 3.2 13.5 - - - +
206A LEU* 1.3 91.5 - - + +
208A VAL* 1.3 61.8 + - - +
209A ASP* 6.5 1.6 - - - -
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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
----------------------------------------------------------
195A LEU* 3.7 26.7 - - + -
196A SER 3.5 3.8 - - - -
197A VAL* 3.9 6.7 - - + -
205A LEU* 4.1 23.1 - - + -
207A LYS* 1.3 76.6 - - - +
209A ASP* 1.3 65.9 + - - +
210A VAL* 4.5 2.0 - - + -
286A LEU* 5.5 1.1 - - + +
287A SER* 3.3 29.2 + - - +
288A ASP 3.3 28.7 - - - +
289A ASP* 4.6 2.0 - - - -
290A LEU* 4.1 22.9 - - + +
294A LEU* 5.0 2.0 - - + -
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Residues in contact with ASP 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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194A ARG* 3.6 1.4 - - - +
195A LEU* 3.5 3.8 - - - +
196A SER* 2.9 50.8 + - - +
207A LYS* 6.5 1.8 - - - -
208A VAL* 1.3 76.2 - - - +
210A VAL* 1.3 64.3 + - - +
211A GLN* 2.9 40.6 + - - +
285A GLN* 4.5 2.4 - - - +
286A LEU 3.6 5.9 - - - +
287A SER* 4.3 9.2 + - - +
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Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU* 3.6 43.5 - - + +
194A ARG 3.3 5.8 - - - +
195A LEU* 3.8 20.2 - - + -
208A VAL* 4.5 1.8 - - + -
209A ASP* 1.3 79.2 - - - +
211A GLN* 1.3 67.0 + - - +
212A GLY 4.5 1.1 - - - +
284A TYR* 4.8 5.4 - - + -
285A GLN* 3.2 9.0 - - - +
286A LEU* 2.9 46.3 + - + +
290A LEU* 3.8 22.9 - - + -
416A CYS* 4.0 7.0 - - + -
417A SER* 4.8 3.6 - - - +
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Residues in contact with GLN 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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192A VAL 3.7 1.6 - - - +
193A GLU* 3.4 0.9 - - - -
194A ARG* 2.9 54.0 + - + +
209A ASP* 2.9 37.5 + - - +
210A VAL* 1.3 74.7 + - - +
212A GLY* 1.3 61.1 + - - +
213A GLU* 5.5 2.3 - - + +
284A TYR 3.7 3.1 - - - +
285A GLN* 3.0 40.5 + - - +
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Residues in contact with GLY 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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192A VAL 3.4 7.0 - - - -
193A GLU* 4.0 3.6 - - - -
210A VAL 4.0 1.4 - - - -
211A GLN* 1.3 75.2 - - - +
213A GLU* 1.3 66.7 + - - +
283A ARG* 3.3 5.9 - - - +
284A TYR* 2.8 61.9 + - - +
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Residues in contact with GLU 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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190A ALA 3.6 1.0 - - - +
191A VAL* 3.5 4.3 - - - +
192A VAL* 2.9 34.8 + - - +
211A GLN* 5.5 2.5 - - + +
212A GLY* 1.3 79.5 - - - +
214A ILE* 1.3 64.0 + - - +
215A ARG* 2.9 42.2 + - + +
280A THR* 4.1 13.5 + - + -
282A MET 3.2 7.4 - - - +
283A ARG* 2.6 42.8 + - + -
284A TYR* 3.8 2.5 - - - -
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Residues in contact with ILE 214 (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 LEU* 3.5 33.9 - - + -
190A ALA 3.4 5.4 - - - +
191A VAL* 4.4 11.4 - - + -
213A GLU* 1.3 78.1 - - - +
215A ARG* 1.3 59.5 + - - +
228A ILE* 5.0 4.9 - - + -
230A LEU* 3.6 31.0 - - + -
270A LEU* 5.3 2.9 - - + -
280A THR* 3.5 3.5 - - - +
281A VAL* 2.8 35.4 + - + +
282A MET* 2.8 42.0 + - + +
284A TYR* 4.4 12.6 - - + -
419A LEU* 5.1 3.4 - - + -
421A VAL* 4.4 11.2 - - + -
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Residues in contact with ARG 215 (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 PHE 4.5 0.2 - - - -
189A LEU* 3.2 7.1 - - - +
190A ALA* 2.8 47.3 + - + +
192A VAL* 3.8 40.5 + - + +
213A GLU* 2.9 34.9 + - + +
214A ILE* 1.3 77.5 - - - +
216A LEU* 1.3 61.2 + - - +
278A GLU* 6.5 0.4 - - + -
279A LEU 3.5 7.4 - - - +
280A THR* 4.0 14.3 + - - +
445A HIS* 5.9 2.0 - - - -
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Residues in contact with LEU 216 (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 VAL* 3.5 26.7 - - + -
188A PHE 3.5 6.7 - - - +
189A LEU* 3.9 14.8 - - + -
214A ILE 4.3 0.2 + - - -
215A ARG* 1.3 76.6 - - - +
217A LYS* 1.3 61.8 + - - +
218A SER* 4.3 5.2 - - - +
226A MET* 3.3 37.5 - - + -
228A ILE* 5.0 0.4 - - + -
272A LEU* 4.3 7.9 - - + -
274A PRO* 3.8 24.5 - - + -
277A GLY 3.7 1.0 - - - +
278A GLU* 3.2 4.7 - - - +
279A LEU* 2.7 44.2 + - + +
281A VAL* 3.8 25.1 - - + -
424A LEU* 4.8 0.7 - - + -
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Residues in contact with LYS 217 (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 VAL* 3.5 1.4 - - - +
188A PHE* 2.8 72.1 + - + +
216A LEU* 1.3 75.2 - - - +
218A SER* 1.3 65.7 + - - +
219A PHE* 4.0 24.7 - - + -
277A GLY* 3.3 10.5 - - - +
278A GLU* 3.9 29.7 + - + +
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Residues in contact with SER 218 (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 GLU 3.8 4.9 - - - -
187A VAL* 4.0 26.7 - - - -
216A LEU* 4.3 3.6 - - - +
217A LYS* 1.3 77.9 - - - +
219A PHE* 1.3 67.1 + - - +
220A LEU* 3.9 10.8 + - - +
226A MET* 4.3 2.2 - - - +
274A PRO* 3.5 30.5 - - - +
275A PRO 3.6 2.9 + - - +
276A GLN* 3.5 4.2 - - - -
277A GLY 2.7 36.1 + - - -
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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