Contacts of the helix formed by residues 154 - 162 (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 GLU 154 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C LYS* 5.3 7.9 + - - -
50C TYR* 4.3 13.8 + - - -
151I GLY* 3.5 17.0 - - - +
152I GLU 2.5 6.3 + - - -
153I ALA* 1.3 77.3 - - - +
155I ARG* 1.3 64.3 + - - +
156I LEU 3.2 2.6 + - - -
157I ARG* 3.6 51.7 + - - +
158I ALA 4.6 0.5 + - - -
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Residues in contact with ARG 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TYR* 2.7 29.7 + - - +
50C TYR* 3.6 35.2 - - + +
96D GLY 4.1 5.7 + - - -
97D GLY* 3.8 23.0 - - - -
105D THR* 6.5 0.2 - - - -
151I GLY 3.6 3.1 + - - +
152I GLU* 2.6 55.1 + - - +
154I GLU* 1.3 76.2 + - - +
156I LEU* 1.3 62.5 + - - +
157I ARG 3.3 0.2 - - - -
158I ALA* 3.7 13.2 + - - +
159I TYR 4.1 1.9 + - - -
3Q TYR* 3.2 22.6 + - - -
4Q LYS* 2.9 49.9 + - - +
5Q PHE 4.7 0.4 - - - -
6Q TYR* 4.5 4.8 - - - +
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Residues in contact with LEU 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I GLN* 3.8 38.1 - - + +
126I LEU* 3.6 29.8 - - + -
133I TRP* 4.4 11.9 - - + -
147I TRP* 5.5 2.2 - - + -
152I GLU* 3.5 9.3 + - + +
153I ALA 5.1 4.7 - - - +
154I GLU 3.2 1.5 - - - -
155I ARG* 1.3 76.7 - - - +
157I ARG* 1.3 67.8 - - + +
159I TYR* 3.1 7.1 + - + +
160I LEU* 2.7 47.3 + - + +
3Q TYR* 4.0 32.0 + - + +
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Residues in contact with ARG 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H GLU* 4.6 20.2 + - - +
130I LEU* 3.6 33.2 + - + +
131I LYS* 3.8 24.5 - - - +
153I ALA 5.4 1.3 + - - +
154I GLU* 3.6 47.5 + - - +
156I LEU* 1.3 77.5 - - + +
158I ALA* 1.3 61.2 + - - +
160I LEU* 4.3 4.0 - - - -
161I GLU* 2.4 65.7 + - - +
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Residues in contact with ALA 158 (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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31C TYR* 5.6 2.9 - - + +
50C TYR* 3.2 46.4 - - + -
51C SER* 3.8 17.4 + - - +
154I GLU 4.6 0.6 + - - -
155I ARG* 3.7 7.2 + - + +
157I ARG* 1.3 77.2 - - - +
159I TYR* 1.3 54.8 + - - +
161I GLU* 5.3 0.4 - - - -
162I GLY* 2.7 34.6 + - - +
163I THR* 3.1 5.1 + - - +
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Residues in contact with TYR 159 (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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31C TYR* 6.0 0.9 - - - +
7I TYR* 3.3 20.4 - - - -
99I SER* 4.3 13.4 + - - -
100I GLY 5.6 0.7 - - - -
155I ARG 4.1 0.2 + - - -
156I LEU* 3.1 8.5 + - + +
158I ALA* 1.3 78.5 - - - +
160I LEU* 1.3 80.2 + - + +
163I THR* 3.0 37.6 + - + +
164I CYS* 2.4 47.7 + - + -
1Q GLU 2.8 28.8 + - - -
2Q GLN* 3.3 12.1 + - - -
3Q TYR* 3.1 59.7 + + + -
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Residues in contact with LEU 160 (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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99I SER* 5.3 2.9 - - - +
100I GLY 3.7 31.2 - - - +
101I CYS* 4.1 5.7 - - + +
109I LEU* 5.0 5.7 - - + +
112I GLY* 4.6 17.3 - - - -
113I TYR 4.3 13.9 - - - +
114I GLN* 6.5 0.2 - - + -
126I LEU* 4.8 0.9 - - + -
130I LEU* 4.6 13.7 - - + -
156I LEU* 2.7 54.7 + - + +
157I ARG* 2.9 3.8 + - - +
159I TYR* 1.3 96.0 - - + +
161I GLU* 1.3 61.5 + - + +
164I CYS* 3.5 8.4 - - + +
165I VAL* 3.3 19.4 - - - +
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Residues in contact with GLU 161 (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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221H GLY 5.1 6.6 - - - +
109I LEU* 4.7 20.2 - - + +
130I LEU* 5.2 10.9 - - + +
157I ARG* 2.4 56.2 + - - +
158I ALA* 5.3 0.2 - - - -
160I LEU* 1.3 73.3 - - + +
162I GLY* 1.3 56.8 + - - +
165I VAL* 3.8 16.2 - - - +
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Residues in contact with GLY 162 (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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51C SER* 5.1 5.8 - - - -
52C GLY 5.4 3.6 - - - -
158I ALA* 2.7 18.1 + - - +
161I GLU* 1.3 74.9 - - - +
163I THR* 1.3 67.0 + - - -
164I CYS 3.0 2.4 + - - -
165I VAL* 3.3 3.5 + - - +
166I GLU* 2.7 40.7 + - - +
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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