Contacts of the strand formed by residues 142 - 152 (chain B) 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 LYS 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A MET* 3.6 22.5 - - + +
172A ALA* 5.4 4.0 - - - +
175A SER* 4.3 13.6 + - - +
136B GLU* 3.5 7.5 - - - +
137B ILE* 3.1 28.3 + - - +
140B LYS* 3.0 23.6 - - + +
141B GLN* 1.3 81.6 - - - +
143B ALA* 1.3 60.0 + - - +
197B ARG* 3.2 45.8 - - + +
198B VAL 3.4 9.9 - - - +
199B SER* 4.5 2.9 - - - -
200B ALA 4.2 0.7 - - - +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PRO* 4.0 20.9 - - + -
136B GLU* 3.8 2.2 - - - -
137B ILE* 4.1 5.8 - - + -
142B LYS* 1.3 76.6 - - - +
144B THR* 1.3 61.2 + - - +
145B LEU* 3.6 3.0 + - + +
196B LEU 3.3 2.9 - - - +
197B ARG* 3.0 23.3 - - - -
198B VAL* 2.6 22.6 + - + +
199B SER 3.8 10.1 - - - +
200B ALA* 4.9 0.2 - - - -
203B TRP* 3.9 19.5 - - + -
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Residues in contact with THR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 3.4 19.6 - - - +
142A LEU* 3.5 23.4 - - + +
144A THR* 5.1 0.5 + - - +
132B PRO* 3.7 10.3 - - - +
136B GLU* 2.6 35.2 + - - +
143B ALA* 1.3 72.3 - - - +
145B LEU* 1.3 72.1 + - - +
146B VAL* 5.1 2.0 - - + -
195B ARG* 3.8 31.3 + - + +
196B LEU 3.6 4.5 - - - +
197B ARG* 3.1 21.0 + - + +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU* 4.4 17.0 - - + -
130B PHE 3.8 7.4 - - - +
131B GLU* 5.2 0.7 - - - -
132B PRO* 4.1 17.0 - - + -
143B ALA* 4.1 10.1 - - + +
144B THR* 1.3 75.7 - - - +
146B VAL* 1.3 59.2 + - - +
161B TRP* 4.1 17.3 - - + -
195B ARG* 3.4 4.2 - - - -
196B LEU* 2.8 44.0 + - + +
198B VAL* 4.4 13.0 - - + -
203B TRP* 4.1 27.1 - - + -
210B PHE* 3.8 38.6 - - + -
241B ALA* 4.6 2.7 - - + -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 3.3 25.4 - - + -
140A LEU* 3.8 24.0 - - + -
142A LEU* 5.7 2.0 - - + -
181A ILE* 3.7 26.7 - - + -
129B LEU* 3.8 3.9 - - - -
130B PHE* 2.9 65.8 + - + +
144B THR* 4.8 5.2 - - + +
145B LEU* 1.3 75.1 - - - +
147B CYS* 1.3 69.1 + - - +
148B LEU* 5.0 0.2 - - + -
193B SER* 4.9 1.1 - - - -
194B SER 3.3 9.6 - - - +
195B ARG* 5.1 0.7 - - + -
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Residues in contact with CYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL* 4.4 8.5 - - - -
128B SER 3.9 9.2 - - - -
129B LEU* 4.3 1.3 - - - -
146B VAL* 1.3 72.3 - - - +
148B LEU* 1.3 68.6 + - - +
159B LEU* 4.0 12.2 - - + +
161B TRP* 3.4 20.0 - - + -
192B LEU 4.7 0.2 - - - -
193B SER* 3.0 5.5 - - - -
194B SER* 2.6 39.3 + - - +
212B CYS* 2.0 52.0 - - + -
214B VAL* 4.7 1.3 - - - -
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.8 26.5 - - + -
183A TRP* 4.0 32.5 - - + -
126B LYS 3.8 0.9 - - - +
127B VAL* 3.4 4.3 - - - +
128B SER* 3.2 30.9 + - - +
130B PHE* 4.0 25.6 - - + -
146B VAL 3.9 0.2 + - - -
147B CYS* 1.3 79.4 - - - +
149B ALA* 1.3 72.8 + - - +
150B ARG* 3.9 28.8 + - + +
191B CYS* 4.8 0.2 - - + -
192B LEU 3.5 12.6 - - - +
193B SER* 3.9 14.4 - - - -
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PRO* 4.5 4.5 - - + -
126B LYS 3.4 5.8 - - - +
127B VAL* 4.4 1.6 - - + +
147B CYS* 5.1 0.2 - - - -
148B LEU* 1.3 73.9 - - - +
150B ARG* 1.3 62.1 + - - +
152B PHE* 3.4 18.1 - - + -
159B LEU* 5.0 2.7 - - + -
191B CYS* 3.0 7.3 - - - +
192B LEU* 2.7 47.0 + - + +
214B VAL* 4.2 31.0 - - + -
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Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A THR* 6.1 0.8 - - - +
183A TRP* 3.1 40.9 - - - +
184A SER 6.1 1.0 - - - -
185A ASN* 6.1 1.0 - - - +
125B PRO* 3.5 0.9 - - - +
126B LYS* 2.6 48.5 + - + +
148B LEU* 3.9 21.0 - - + +
149B ALA* 1.3 79.0 - - - +
151B GLY* 1.3 60.3 + - - +
152B PHE* 3.5 4.6 + - - -
181B GLU* 2.5 40.9 + - - +
190B TYR 3.8 4.7 - - - -
191B CYS* 4.1 6.3 - - - -
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Residues in contact with GLY 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B THR* 3.5 21.3 - - - +
124B PRO 3.5 7.2 - - - +
126B LYS* 4.9 4.3 - - - -
150B ARG* 1.3 74.1 - - - +
152B PHE* 1.3 62.4 + - - +
181B GLU* 3.6 6.3 + - - -
187B TYR 4.9 1.9 - - - +
189B SER* 3.6 16.2 + - - -
190B TYR 3.4 6.3 + - - -
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B THR 2.9 15.9 - - - +
124B PRO 3.7 1.1 + - - -
125B PRO* 3.5 30.1 - - + -
149B ALA* 3.4 27.1 - - + -
150B ARG 3.5 4.9 + - - -
151B GLY* 1.3 74.7 - - - +
153B PHE* 1.3 64.1 + - - +
154B PRO 4.4 0.4 - - - -
155B ASP* 4.1 8.3 - - - -
157B VAL* 4.0 30.7 - - + -
178B ALA* 4.2 4.5 - - + -
189B SER* 3.6 1.0 - - - -
190B TYR* 2.7 73.8 + + + -
191B CYS 3.7 10.3 - - - -
192B LEU* 4.1 10.1 - - + -
216B PHE* 3.9 11.0 - - + -
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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