Contacts of the strand formed by residues 215 - 231 (chain A) in PDB entry 1M4U
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 CYS 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ILE 4.5 3.6 - - - -
205A TRP* 3.2 40.4 - - + -
206A ARG 3.1 5.4 - - - +
207A CYS* 2.1 44.2 - - - -
212A GLY 3.1 21.1 - - - -
214A ARG* 1.3 74.8 - - - +
216A GLY* 1.3 57.7 + - - +
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Residues in contact with GLY 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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204A ARG 3.0 1.4 - - - +
205A TRP* 3.3 16.7 - - - -
206A ARG* 2.6 41.9 + - - +
215A CYS* 1.3 75.1 - - - +
217A TRP* 1.3 58.8 + - - -
218A ILE* 4.9 3.1 - - - -
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Residues in contact with TRP 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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56A PRO* 3.9 15.0 - - + -
60A ASP* 3.1 30.0 + - - -
61A LEU* 3.6 25.6 - - + -
66A LEU* 3.9 21.1 - - + +
69A LEU* 4.0 28.8 - - + +
166A SER 3.8 20.0 - - - -
167A ARG 3.6 18.4 - - - -
168A PHE 4.3 0.2 - - - -
169A TRP* 3.6 26.0 - - + -
203A LEU* 3.6 24.7 - - + -
204A ARG 3.0 21.8 - - - -
205A TRP* 3.6 22.1 - + - -
216A GLY* 1.3 69.9 - - - -
218A ILE* 1.4 67.4 + - - +
219A PRO* 4.9 0.2 - - - +
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Residues in contact with ILE 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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203A LEU* 3.3 7.3 - - - -
204A ARG* 3.0 35.6 + - + +
206A ARG* 3.8 35.4 - - + +
216A GLY 4.9 2.9 - - - +
217A TRP* 1.4 79.2 - - - +
219A PRO* 1.3 81.2 - - + +
220A ILE* 3.3 12.6 + - + +
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Residues in contact with PRO 219 (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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69A LEU* 5.9 7.2 - - + +
70A LEU* 5.8 1.8 - - + -
73A HIS* 5.6 5.4 - - + +
201A THR* 4.1 16.8 - - + -
202A VAL 3.4 8.1 - - - +
203A LEU* 4.2 10.7 - - + -
218A ILE* 1.3 93.6 - - + +
220A ILE* 1.3 62.6 + - - +
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Residues in contact with ILE 220 (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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168A PHE* 3.9 29.2 - - + -
200A LEU 3.4 0.5 - - - +
201A THR* 3.3 7.0 - - - +
202A VAL* 2.8 46.1 + - + +
204A ARG* 3.6 19.7 - - + -
218A ILE* 3.6 18.4 - - + +
219A PRO* 1.3 78.3 - - - +
221A GLN* 1.3 76.5 + - - +
222A TYR* 3.8 14.6 - - + +
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Residues in contact with GLN 221 (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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199A HIS* 4.0 36.5 + - + +
200A LEU 3.5 3.1 - - - -
201A THR* 4.4 13.7 + - + +
220A ILE* 1.3 78.4 - - - +
222A TYR* 1.4 58.0 + - - +
223A PRO* 4.0 5.9 - - - +
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Residues in contact with TYR 222 (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 LEU* 5.9 5.1 - - + +
45A ASP* 2.5 27.4 + - - -
162A ASN* 3.4 14.6 + - - -
164A LEU* 3.5 31.6 - - + -
168A PHE* 5.0 8.5 - + - -
173A VAL* 4.3 8.5 - - + -
175A VAL* 4.0 20.8 - - + +
199A HIS* 3.3 1.7 - - - -
200A LEU* 2.7 49.0 + - + +
202A VAL* 5.3 6.3 - - + -
220A ILE* 3.7 16.8 + - + -
221A GLN* 1.4 71.5 - - - +
223A PRO* 1.3 87.7 - - + +
224A ILE* 4.0 6.5 - - + -
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Residues in contact with PRO 223 (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* 4.3 21.3 - - + +
43A LEU* 4.1 31.7 - - + +
175A VAL* 5.4 0.5 - - - +
197A SER* 4.6 2.5 - - - +
198A VAL 3.5 7.4 - - - +
199A HIS* 3.8 21.3 - - + +
221A GLN 4.0 5.6 - - - +
222A TYR* 1.3 105.5 - - + +
224A ILE* 1.3 67.9 + - - +
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Residues in contact with ILE 224 (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* 5.2 2.5 - - - -
78A PHE* 3.5 34.3 - - + -
159A TYR* 4.8 2.7 - - + +
174A LYS 3.9 11.7 - - - +
175A VAL* 4.2 7.9 - - + -
176A GLY 4.5 9.6 - - - +
197A SER* 3.4 5.5 - - - -
198A VAL* 2.8 48.7 + - + +
200A LEU* 3.8 31.0 - - + -
222A TYR* 4.0 13.0 - - + -
223A PRO* 1.3 82.6 - - - +
225A ILE* 1.3 71.6 + - - +
226A SER* 3.3 1.7 + - - -
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Residues in contact with ILE 225 (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* 4.1 20.0 - - + -
42A PRO* 3.8 23.6 - - + -
157A VAL* 3.9 8.3 - - + +
159A TYR* 4.4 2.3 + - - -
176A GLY* 3.6 36.8 + - - +
177A SER* 4.3 14.4 - - - +
178A CYS* 5.0 0.9 - - - +
194A PRO* 3.7 26.0 - - + -
196A LYS 3.8 5.8 - - - +
197A SER* 4.5 1.6 - - - +
224A ILE* 1.3 79.9 - - - +
226A SER* 1.3 60.9 + - - +
227A GLU 3.9 18.8 - - - +
228A CYS* 4.0 16.8 - - - -
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Residues in contact with SER 226 (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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157A VAL* 4.0 13.1 - - - +
159A TYR* 4.9 7.5 + - - -
196A LYS* 3.0 24.3 + - - +
197A SER* 3.6 5.4 + - - -
198A VAL* 4.2 26.2 - - - +
224A ILE* 3.3 3.7 + - - -
225A ILE* 1.3 74.6 - - - +
227A GLU* 1.4 70.6 + - - +
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Residues in contact with GLU 227 (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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157A VAL* 4.2 4.3 - - - -
194A PRO* 3.4 6.2 - - - +
195A SER* 2.7 37.7 + - - +
196A LYS* 3.3 44.7 + - + +
225A ILE* 3.8 2.5 - - - +
226A SER* 1.4 85.0 + - - +
228A CYS* 1.3 65.5 + - - +
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Residues in contact with CYS 228 (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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154A PHE* 5.9 1.0 - - - -
155A CYS* 3.4 36.7 + - + +
156A PRO 4.1 5.6 - - - +
157A VAL* 4.1 6.5 - - - +
177A SER 4.0 7.9 - - - -
178A CYS* 2.2 52.9 - - + -
193A LYS 3.3 5.4 - - - +
195A SER* 3.4 4.8 + - - -
225A ILE* 4.0 8.7 - - - -
227A GLU* 1.3 83.0 - - - +
229A LYS* 1.4 64.4 + - - +
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Residues in contact with LYS 229 (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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155A CYS* 3.7 8.1 - - - -
193A LYS* 2.8 29.5 + - - +
195A SER* 3.8 20.0 - - - -
228A CYS* 1.4 75.7 - - - +
230A CYS* 1.3 75.4 + - - +
231A SER* 3.6 4.5 + - - -
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Residues in contact with CYS 230 (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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153A THR* 3.9 16.7 + - - +
155A CYS* 3.6 4.7 - - - -
184A CYS* 2.1 65.3 - - + +
185A SER* 3.9 3.4 - - - -
190A MET* 3.6 25.0 - - + +
191A VAL 3.8 0.7 - - - -
229A LYS* 1.3 81.0 + - - +
231A SER* 1.3 65.0 + - - +
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Residues in contact with SER 231 (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 MET* 3.4 10.2 - - - -
191A VAL* 2.7 38.4 + - - +
193A LYS* 4.3 16.4 + - - +
229A LYS* 4.0 8.1 - - - -
230A CYS* 1.3 79.0 - - - +
232A CYS* 1.3 75.1 + - - +
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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