Contacts of the strand formed by residues 190 - 199 (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 TYR 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D ALA 4.7 0.2 - - - +
150D ARG* 2.8 26.9 - - - +
151D GLY 3.6 2.6 + - - -
152D PHE* 3.9 11.9 + - + -
153D PHE* 4.4 14.7 - + - -
155D ASP* 3.9 40.2 - - + -
178D ALA* 4.0 18.8 - - + -
179D TYR 3.0 22.7 - - - +
180D LYS* 3.6 44.6 + - + +
186D ASN 5.1 0.7 + - - -
187D TYR* 4.5 7.4 - - - -
189D SER* 1.3 87.6 - - - +
191D CYS* 1.3 59.5 + - - +
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Residues in contact with CYS 191 (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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183C TRP* 5.2 8.7 - - + -
150D ARG* 3.2 18.4 - - + +
178D ALA* 2.9 11.3 - - - +
179D TYR* 2.8 51.7 + - + -
181D GLU* 3.0 52.5 - - - -
190D TYR* 1.3 74.8 - - - +
192D LEU* 1.3 63.1 + - - +
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Residues in contact with LEU 192 (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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183C TRP* 4.7 8.2 - - - -
148D LEU* 4.5 3.3 - - - -
149D ALA 4.2 22.1 + - - +
150D ARG* 3.9 7.8 - - - +
157D VAL* 3.5 33.9 - - + +
159D LEU* 3.6 25.6 - - + -
174D THR* 4.0 8.3 - - + -
175D ASP* 3.1 44.0 - - + +
177D GLN* 3.3 21.5 - - - +
178D ALA* 3.7 9.0 - - + +
179D TYR* 4.6 4.9 - - - -
191D CYS* 1.3 75.3 - - - +
193D SER* 1.3 66.1 + - - +
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Residues in contact with SER 193 (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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163C THR* 4.6 13.0 - - - +
181C ILE* 4.8 5.1 - - - +
183C TRP* 4.9 16.4 - - - -
146D VAL* 4.7 6.1 - - - -
147D CYS 4.1 8.5 - - - -
148D LEU* 5.6 0.7 - - - -
159D LEU* 4.5 4.0 - - - -
173D SER 2.9 14.7 - - - +
174D THR* 4.5 0.9 - - - -
175D ASP* 2.7 36.5 + - - +
179D TYR* 5.3 0.3 - - - -
192D LEU* 1.3 79.1 - - - +
194D SER* 1.3 60.3 + - - +
195D ARG* 2.5 26.5 + - - -
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Residues in contact with SER 194 (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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146D VAL* 2.8 25.4 - - - +
147D CYS* 3.5 9.5 + - - +
159D LEU* 3.2 26.9 - - - +
161D TRP* 3.1 21.7 + - - -
173D SER 3.3 9.0 - - - -
174D THR* 3.7 25.4 - - - -
193D SER* 1.3 72.8 - - - +
195D ARG* 1.3 72.0 + - - +
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Residues in contact with ARG 195 (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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142C LEU* 5.5 0.7 - - - -
163C THR* 6.3 0.6 - - - +
166C THR* 2.6 41.7 + - - +
167C VAL 4.3 0.7 - - - +
168C LEU* 4.1 24.5 - - + -
178C ASN 5.6 0.4 - - - -
179C GLY* 4.4 4.9 - - - -
181C ILE* 3.5 37.7 - - + +
144D THR* 4.8 5.6 - - + -
145D LEU 3.1 20.0 - - - +
146D VAL* 4.4 1.1 - - + -
161D TRP* 3.3 15.2 + - - +
171D GLY 3.1 23.1 - - - -
172D VAL 3.3 3.1 + - - -
173D SER* 3.4 17.9 - - - +
175D ASP* 3.8 3.2 + - - -
193D SER* 2.5 52.7 + - - -
194D SER* 1.3 93.2 + - - +
196D LEU* 1.3 65.9 + - - +
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Residues in contact with LEU 196 (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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168C LEU* 4.6 6.3 - - - -
169C ASP 5.5 2.0 - - - +
143D ALA 3.6 0.2 - - - +
144D THR* 3.7 2.8 - - - +
145D LEU* 2.9 39.1 + - + +
161D TRP* 3.6 40.6 - - + -
163D VAL* 5.3 4.7 - - + -
168D VAL* 5.3 9.4 - - + -
170D SER* 3.4 13.7 - - - +
171D GLY* 3.3 28.7 - - - -
172D VAL 4.4 0.7 - - - +
195D ARG* 1.3 78.6 - - - +
197D ARG* 1.3 73.7 + - - +
198D VAL* 5.0 0.9 - - + -
202D PHE* 6.2 2.0 - - + -
210D PHE* 4.4 20.0 - - + -
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Residues in contact with ARG 197 (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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144C THR* 2.7 18.8 + - - -
145C ASP* 3.0 17.4 + - - -
168C LEU* 4.1 15.5 - - + +
169C ASP 5.3 8.0 + - - +
170C MET* 4.7 18.3 - - + +
174C ASP 5.9 0.4 + - - -
175C SER* 5.7 4.8 - - - +
176C LYS 6.0 0.2 - - - +
177C SER* 2.7 38.2 + - - +
140D LYS* 4.6 3.0 - - - +
142D LYS* 2.9 59.5 - - + +
143D ALA 3.2 12.0 - - - +
144D THR* 4.1 5.5 + - - -
171D GLY* 5.1 0.6 - - - -
196D LEU* 1.3 85.5 - - - +
198D VAL* 1.3 77.8 + - - +
199D SER* 4.3 1.5 + - - +
202D PHE* 4.1 10.4 - - - -
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Residues in contact with VAL 198 (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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132D PRO* 5.8 0.2 - - + -
141D GLN 3.6 0.7 - - - +
142D LYS 3.7 0.7 - - - -
143D ALA* 3.0 42.9 + - + +
145D LEU* 3.6 16.6 - - + -
196D LEU* 5.0 2.2 - - + -
197D ARG* 1.3 82.5 - - - +
199D SER* 1.3 66.4 + - - +
202D PHE* 3.4 21.1 - - + -
203D TRP* 3.3 23.8 - - + -
204D HIS* 4.4 0.7 - - + -
210D PHE* 3.4 37.7 - - + -
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Residues in contact with SER 199 (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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170C MET* 3.9 26.0 - - - +
141D GLN* 2.8 16.2 - - - -
142D LYS* 4.6 6.2 + - - +
197D ARG* 4.3 2.6 + - - +
198D VAL* 1.3 78.5 - - - +
200D ALA* 1.3 68.8 + - - +
201D THR* 4.7 3.4 - - - -
202D PHE* 3.1 37.8 - - - +
204D HIS* 3.3 9.9 + - - -
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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