Contacts of the strand formed by residues 209 - 216 (chain D) 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 HIS 209 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D VAL* 3.2 27.8 - - - +
164D ASN* 2.9 48.5 + - - +
208D ASN* 1.3 80.6 + - - +
210D PHE* 1.3 75.9 + - - +
211D ARG* 3.1 40.9 + - + +
240D GLU* 3.9 14.5 + - + -
241D ALA 4.0 6.7 + - - -
242D TRP* 5.1 14.2 + + + +
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Residues in contact with PHE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D LEU* 4.6 8.7 - - + -
161D TRP* 4.8 8.3 - + + -
162D TRP 3.5 2.2 - - - -
163D VAL* 4.8 9.2 - - + -
196D LEU* 4.4 19.3 - - + -
198D VAL* 3.4 34.5 - - + -
202D PHE* 4.8 7.0 - + - -
203D TRP* 3.4 31.4 - + - -
208D ASN* 3.0 31.2 - - - -
209D HIS* 1.3 88.1 + - - +
211D ARG* 1.3 74.0 + - - +
240D GLU* 3.9 4.9 - - - +
241D ALA* 3.6 40.8 + - + +
242D TRP 4.1 7.9 - - - -
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Residues in contact with ARG 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D TRP* 3.2 14.1 - - - -
162D TRP* 2.7 67.5 + - + +
164D ASN 4.2 11.9 - - - -
209D HIS* 3.1 33.7 + - + +
210D PHE* 1.3 88.7 - - - +
212D CYS* 1.3 63.7 + - - +
213D GLN* 5.6 7.3 - - - +
238D SER* 4.9 14.1 + - - -
240D GLU* 4.1 21.7 - - - +
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Residues in contact with CYS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D VAL* 4.0 8.1 - - - -
129D LEU* 4.9 4.0 - - + -
147D CYS* 2.0 53.4 - - + -
148D LEU 4.5 3.1 - - - -
159D LEU* 4.9 4.7 - - - -
160D SER 3.2 11.7 - - - +
161D TRP* 5.0 7.0 - - + -
162D TRP* 4.0 1.6 - - - -
194D SER* 5.3 0.2 - - - -
211D ARG* 1.3 80.3 + - - +
213D GLN* 1.3 68.9 + - - +
238D SER* 3.4 20.4 - - - -
239D ALA 3.3 21.8 + - - +
240D GLU* 5.1 0.4 - - - +
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Residues in contact with GLN 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLU 4.0 0.2 - - - +
159D LEU* 3.2 8.3 - - - +
160D SER* 3.1 31.2 + - - -
162D TRP* 3.1 43.4 - - + +
211D ARG* 5.6 6.8 - - - +
212D CYS* 1.3 76.0 - - - +
214D VAL* 1.3 69.2 + - - +
215D GLN* 3.8 3.7 + - + +
236D ASN* 3.0 40.4 + - + +
237D ILE 4.1 9.6 - - - +
238D SER* 4.6 4.7 - - - +
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Residues in contact with VAL 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D PRO* 3.5 31.2 - - + -
127D VAL* 3.5 22.7 - - + -
148D LEU 3.4 12.3 - - - +
149D ALA* 3.2 35.7 - - + -
157D VAL* 4.1 17.5 - - + -
159D LEU* 4.7 4.9 - - + +
213D GLN* 1.3 74.5 - - - +
215D GLN* 1.3 51.1 + - - +
216D PHE* 2.5 23.2 + - - +
236D ASN* 3.8 11.8 - - - -
237D ILE 3.2 14.6 + - - +
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Residues in contact with GLN 215 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C ARG* 4.2 14.0 + - - +
156D HIS 3.6 6.6 - - - +
157D VAL* 3.8 6.9 - - - -
158D GLU* 3.2 40.3 + - - +
162D TRP* 6.2 2.2 - - - -
213D GLN* 3.8 6.1 + - + +
214D VAL* 1.3 66.9 - - - +
216D PHE* 1.3 59.6 + - - +
217D HIS* 3.0 34.7 + - + +
236D ASN* 4.2 19.7 - - - +
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Residues in contact with PHE 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D VAL* 5.3 0.2 - - + -
123D THR 3.8 5.6 - - - -
124D PRO* 4.2 0.7 - - + -
125D PRO* 3.2 39.9 - - + -
152D PHE* 3.8 7.6 - + - -
154D PRO* 3.3 45.5 - - + -
157D VAL* 4.0 6.1 - - + -
214D VAL 2.5 9.3 + - - +
215D GLN* 1.3 71.0 - - - +
217D HIS* 1.3 66.7 + - - +
218D GLY* 3.7 13.9 + - - -
232D PRO* 3.7 25.6 - - + -
233D VAL 3.0 29.2 - - - -
234D THR* 4.0 11.8 - - - +
235D GLN* 3.1 41.8 + - + +
236D ASN* 4.6 0.9 - - - +
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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