Contacts of the strand formed by residues 241 - 250 (chain I) in PDB entry 1MWA
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 PHE 241 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207I GLY 3.1 22.9 + - - -
208I PHE* 3.0 40.8 + - + -
209I TYR* 4.1 13.9 - + - -
211I ALA* 3.7 26.5 - - + -
233I THR* 3.8 16.2 - - + -
234I ARG* 3.2 9.2 - - - +
235I PRO* 3.5 39.0 - - + -
236I ALA 4.1 0.9 - - - +
239I GLY* 2.9 24.5 - - - -
240I THR* 1.3 73.2 - - - +
242I GLN* 1.3 66.3 + - - +
26M TYR* 5.2 4.3 - - - -
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Residues in contact with GLN 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204I TRP* 5.7 2.0 - - + -
205I ALA 3.2 13.2 - - - +
206I LEU* 3.1 29.8 - - + +
207I GLY 4.6 1.5 - - - +
208I PHE* 3.5 4.3 - - - -
233I THR* 3.7 4.0 - - - +
234I ARG* 2.8 71.4 + - - +
236I ALA* 4.4 12.7 - - + +
241I PHE* 1.3 79.9 - - - +
243I LYS* 1.3 66.3 + - - +
10M TYR* 3.3 15.2 - - - -
11M SER 3.9 4.7 + - - +
12M ARG* 3.2 28.1 + - - +
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Residues in contact with LYS 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204I TRP* 3.7 2.0 - - - +
205I ALA* 2.9 28.7 + - + +
208I PHE* 3.9 9.6 - - + -
213I ILE* 3.8 21.7 + - + +
214I THR* 6.2 0.4 - - - +
215I LEU* 3.8 20.6 - - + +
230I LEU* 3.5 32.2 - - - +
231I VAL* 2.8 38.7 + - + +
232I GLU* 4.1 2.0 - - - +
233I THR* 3.3 29.6 + - - +
234I ARG* 5.8 1.1 - - - +
242I GLN* 1.3 80.1 - - - +
244I TRP* 1.3 71.1 + - - +
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Residues in contact with TRP 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I ARG* 3.3 31.4 - - + -
203I CYS 2.9 19.1 - - - +
204I TRP* 3.2 40.7 - + + -
215I LEU* 3.7 5.6 - - - -
229I GLU* 3.9 20.6 - - + -
230I LEU* 3.9 3.0 - - - +
231I VAL* 3.3 46.5 + - + +
234I ARG* 3.8 11.5 - - - +
243I LYS* 1.3 79.0 - - - +
245I ALA* 1.3 65.3 + - - +
246I SER* 3.2 20.6 - - - -
99M MET* 3.7 48.5 + - + -
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Residues in contact with ALA 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203I CYS* 2.7 30.6 + - + +
215I LEU* 3.9 15.1 - - + +
217I TRP* 3.1 11.2 + - + +
228I MET* 3.5 20.2 - - + -
229I GLU 3.2 7.4 - - - +
230I LEU* 3.2 28.7 - - + -
244I TRP* 1.3 74.9 - - - +
246I SER* 1.3 60.4 + - - +
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Residues in contact with SER 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I THR* 5.0 5.1 - - - -
201I LEU 2.7 21.5 - - - -
202I ARG* 3.7 25.2 + - - -
217I TRP* 3.6 4.9 - - - +
228I MET* 3.1 8.8 - - - +
229I GLU* 2.8 37.2 + - - +
244I TRP* 3.2 18.7 - - - -
245I ALA* 1.3 75.2 - - - +
247I VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I THR* 3.2 4.8 - - - -
201I LEU* 2.9 33.3 + - + -
217I TRP* 3.8 33.4 - - + -
224I LEU* 3.9 23.8 - - + -
227I ASP* 4.6 3.6 - - + +
228I MET* 3.8 23.6 - - + +
229I GLU* 5.0 0.4 - - - +
246I SER* 1.3 77.1 - - - +
248I VAL* 1.3 74.1 + - - +
249I VAL* 3.9 17.9 + - + -
257I TYR* 4.5 3.8 - - + -
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Residues in contact with VAL 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194I ARG* 2.7 37.9 - - - +
198I LYS* 4.0 23.1 - - + +
199I VAL 3.5 8.5 - - - +
200I THR* 4.2 12.8 - - + -
227I ASP* 4.3 22.3 + - - +
229I GLU* 6.2 4.3 - - + -
247I VAL* 1.3 82.8 - - - +
249I VAL* 1.3 67.6 + - - +
257I TYR* 4.7 3.1 + - - -
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Residues in contact with VAL 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198I LYS* 3.3 9.7 - - - +
199I VAL* 2.8 44.8 + - + +
201I LEU* 4.4 6.5 - - + -
247I VAL* 3.9 13.2 - - + +
248I VAL* 1.3 80.6 - - - +
250I PRO* 1.3 81.1 - - + +
254I GLU* 4.0 27.4 - - + -
257I TYR* 3.2 42.8 - - + -
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Residues in contact with PRO 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197I ASP 3.9 5.4 - - - +
198I LYS* 4.5 8.3 - - + -
199I VAL* 4.6 0.2 - - - -
249I VAL* 1.3 95.5 - - + +
251I LEU* 1.3 66.9 + - - +
252I GLY 3.3 0.2 + - - -
253I LYS* 3.1 54.1 + - + +
254I GLU* 3.7 5.7 + - - +
257I TYR* 3.7 13.7 - - - +
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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