Contacts of the strand formed by residues 241 - 250 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207H GLY 3.1 24.1 + - - -
208H PHE* 2.8 49.7 + - + +
209H TYR* 4.3 13.7 - + - -
211H ALA* 3.7 34.3 - - + -
233H THR* 3.8 7.2 - - + -
234H ARG 3.4 20.4 - - - +
235H PRO* 3.9 20.4 - - + -
239H GLY* 3.8 17.0 - - - -
240H THR* 1.3 78.8 - - - +
242H GLN* 1.3 64.7 + - - +
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Residues in contact with GLN 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H TRP* 6.3 0.2 - - + -
205H ALA 3.2 7.2 - - - -
206H LEU* 3.6 17.9 - - + +
207H GLY 5.1 1.1 - - - +
208H PHE* 3.6 2.5 - - - -
233H THR* 3.1 2.8 - - - +
234H ARG* 2.8 73.0 + - + +
236H ALA* 3.7 22.8 - - + +
241H PHE* 1.3 78.8 - - - +
243H LYS* 1.3 65.9 + - - +
10L TYR* 3.4 11.9 - - - -
11L SER 3.2 10.8 + - - -
12L ARG 3.0 28.1 + - - -
901L GOL 3.6 12.6 + - - -
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Residues in contact with LYS 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H TRP* 4.5 1.7 - - - +
205H ALA* 2.7 37.8 + - + +
206H LEU* 4.7 0.6 - - - +
208H PHE* 4.0 12.3 - - + -
213H ILE* 3.8 19.3 - - + -
214H THR* 5.9 0.4 - - - +
215H LEU* 3.6 21.8 - - + +
230H LEU* 4.5 23.0 - - - +
231H VAL* 2.9 37.8 + - - +
232H GLU* 3.6 1.8 - - - +
233H THR* 2.9 34.7 + - - +
234H ARG* 5.6 2.0 - - - +
242H GLN* 1.3 80.2 - - - +
244H TRP* 1.3 69.9 + - - +
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Residues in contact with TRP 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202H ARG* 3.3 37.2 - - + -
203H CYS 3.1 16.4 - - - +
204H TRP* 3.4 37.5 - + + -
215H LEU* 3.7 4.0 - - - -
229H GLU* 3.7 31.0 - - + -
230H LEU* 3.5 5.9 - - - +
231H VAL* 3.4 48.9 + - + +
234H ARG* 4.0 9.4 - - - +
243H LYS* 1.3 80.0 - - - +
245H ALA* 1.3 67.8 + - - +
246H SER* 3.4 22.2 - - - -
99L MET* 3.3 46.1 + - + +
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Residues in contact with ALA 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203H CYS* 2.8 31.8 + - + +
215H LEU* 3.8 25.3 - - + +
216H THR 5.3 0.2 - - - +
217H TRP* 3.3 12.4 + - + +
228H MET* 4.2 15.7 - - + -
229H GLU 3.3 10.3 - - - +
230H LEU* 4.0 11.2 - - + -
244H TRP* 1.3 78.7 - - - +
246H SER* 1.3 61.7 + - - +
259H CYS* 5.8 0.4 - - - -
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Residues in contact with SER 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H THR* 4.1 8.7 - - - +
201H LEU 3.2 16.4 - - - -
202H ARG* 3.7 26.2 + - - -
217H TRP* 3.7 5.2 - - - +
227H ASP 4.4 0.2 - - - +
228H MET* 3.1 8.3 - - - +
229H GLU* 2.8 41.2 + - - +
244H TRP* 3.4 13.9 - - - -
245H ALA* 1.3 74.5 - - - +
247H VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H VAL 3.7 0.7 - - - +
200H THR* 3.6 3.9 - - - +
201H LEU* 3.2 28.5 + - + +
217H TRP* 3.8 38.1 - - + -
224H LEU* 3.8 26.0 - - + -
227H ASP* 4.3 12.6 - - + +
228H MET* 4.5 6.7 - - + -
246H SER* 1.3 76.8 - - - +
248H VAL* 1.3 77.5 + - + +
249H VAL* 3.9 16.7 + - + +
257H TYR* 4.5 3.1 - - + -
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Residues in contact with VAL 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H ARG* 3.6 38.8 - - - +
198H LYS* 5.7 9.0 - - + -
199H VAL 3.3 6.7 - - - +
200H THR* 4.3 7.0 - - + +
227H ASP* 4.5 26.3 + - + +
247H VAL* 1.3 82.7 - - + +
249H VAL* 1.3 62.8 - - - +
250H PRO* 4.8 0.5 - - - +
257H TYR* 5.2 0.7 + - - -
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Residues in contact with VAL 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198H LYS* 3.6 4.8 - - - -
199H VAL* 2.7 38.3 + - + +
201H LEU* 4.1 8.7 - - + -
247H VAL* 4.1 13.7 - - + -
248H VAL* 1.3 78.8 - - - +
250H PRO* 1.3 72.1 - - + +
254H GLU* 3.1 37.9 - - + -
257H TYR* 3.1 47.8 - - + -
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Residues in contact with PRO 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197H ASP 4.2 5.2 - - - +
198H LYS* 4.2 11.9 - - + -
248H VAL 4.8 0.2 - - - +
249H VAL* 1.3 91.4 - - + +
251H LEU* 1.3 58.0 + - - +
253H LYS* 3.5 24.8 + - + +
254H GLU* 2.5 24.1 - - - +
257H TYR* 4.2 10.8 - - - +
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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