Contacts of the strand formed by residues 130 - 137 (chain A) in PDB entry 1MA1
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 GLY 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ALA* 5.0 3.4 - - - -
128A GLY 3.5 3.4 + - - -
129A SER* 1.3 74.9 - - - +
131A TRP* 1.3 67.1 + - - -
148A VAL 2.9 14.1 - - - -
150A LYS 3.7 12.1 - - - -
167A VAL* 2.9 35.0 + - - +
168A TRP* 3.2 10.0 + - - +
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Residues in contact with TRP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.4 43.8 - - + +
80A HIS* 3.6 35.7 - + - -
83A PHE* 3.9 4.0 - - + -
122A ALA 5.2 1.6 - - - -
126A ALA* 5.1 1.0 - - - +
130A GLY* 1.3 75.0 - - - -
132A ALA* 1.3 58.2 + - - +
133A VAL* 4.0 16.6 - - + -
147A GLN* 3.5 9.9 - - - +
148A VAL* 2.7 38.5 + - + +
150A LYS 3.0 20.2 + - - -
151A HIS* 3.0 24.4 + + - -
164A VAL* 3.4 34.5 - - + -
165A LEU 3.4 6.7 - - - +
166A ASP* 3.3 47.6 - - + -
167A VAL* 4.4 4.3 - - - -
168A TRP* 3.3 4.2 - - - +
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Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 3.3 32.7 - - + +
122A ALA* 4.0 9.9 - - + -
123A ALA* 3.9 32.2 - - + +
131A TRP* 1.3 73.2 - - - +
133A VAL* 1.3 63.3 + - - +
145A ILE* 4.9 0.2 - - + -
146A MET 3.7 4.0 - - - -
165A LEU* 2.9 33.9 + - + -
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 4.2 7.4 - - + -
119A PHE* 3.8 4.7 - - - -
131A TRP* 4.0 10.1 - - + -
132A ALA* 1.3 81.4 - - - +
134A LEU* 1.3 72.1 + - - +
135A THR* 5.1 1.8 - - - -
145A ILE* 3.4 3.7 - - - +
146A MET* 2.9 53.4 + - + +
148A VAL* 4.0 22.4 - - + -
161A ILE* 4.1 17.0 - - + -
163A LEU 3.2 9.4 - - - +
164A VAL* 3.6 21.8 - - + -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.6 13.5 - - + -
105A ILE* 5.1 3.1 - - + -
109A PHE* 4.5 1.8 - - + -
115A PHE* 4.0 32.3 - - + -
119A PHE* 3.6 9.6 - - + -
133A VAL* 1.3 79.2 - - - +
135A THR* 1.3 69.7 + - - +
143A LEU* 4.1 22.7 - - + -
144A PHE 3.2 22.0 - - - +
145A ILE* 4.1 5.8 - - + -
161A ILE 4.0 0.2 - - - -
162A LEU* 3.0 43.7 + - + -
163A LEU* 2.8 29.0 + - + +
193A TRP* 5.6 0.9 - - + -
196A VAL* 5.1 3.4 - - + -
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A VAL* 5.1 2.5 - - - -
134A LEU* 1.3 74.3 - - - +
136A TYR* 1.3 70.2 + - - +
143A LEU* 3.3 13.0 - - - +
144A PHE* 2.8 45.9 + - + +
146A MET* 3.7 35.9 - - + -
159A PHE* 3.5 13.7 - - + +
160A ARG 2.6 37.3 + - - -
162A LEU* 4.1 7.2 - - - -
203A ILE* 5.9 0.2 - - - +
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 4.0 12.8 + + - -
135A THR* 1.3 86.2 + - - +
137A CYS* 1.3 57.5 + - - +
138A GLN* 3.2 49.6 + - + +
141A ASP* 2.5 50.3 + - - +
142A ARG 3.4 17.7 - - - -
143A LEU* 4.2 3.6 - - + -
144A PHE 4.4 0.2 - - - +
159A PHE* 3.5 16.9 - - - +
160A ARG 4.5 2.0 + - - -
162A LEU* 4.3 9.0 - - + -
200A PHE* 4.0 15.7 - + - -
203A ILE* 3.9 48.1 - - + +
204A LEU 4.5 11.6 - - - -
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Residues in contact with CYS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TYR* 1.3 72.5 - - - +
138A GLN* 1.3 57.9 + - - +
139A ARG* 3.1 17.2 + - - -
140A THR* 3.3 35.0 - - - +
141A ASP* 2.5 36.9 + - - -
142A ARG 2.8 11.4 + - - +
144A PHE* 3.6 27.7 - - + -
159A PHE* 3.6 19.9 - - + -
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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