Contacts of the strand formed by residues 137 - 144 (chain A) in PDB entry 1MMM
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ASP* 3.7 34.9 + - - +
133A LEU* 3.8 5.3 - - - +
134A LYS* 2.8 41.3 + - + +
135A GLY 3.6 1.0 - - - -
136A ASP* 1.3 80.5 - - - +
138A LEU* 1.3 72.6 + - - +
139A ALA* 4.8 1.5 - - + +
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Residues in contact with LEU 138 (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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98A LEU* 4.2 9.2 - - + -
101A ALA* 3.7 29.6 - - + +
102A ILE* 3.9 27.1 - - + +
104A ARG* 5.2 0.4 - - - +
105A ASP* 3.1 18.8 + - - +
106A PHE* 3.9 21.1 - - + -
131A LEU* 4.1 7.9 - - + -
132A VAL 3.2 13.7 - - - +
133A LEU* 3.9 22.2 - - + -
137A LYS* 1.3 87.2 - - - +
139A ALA* 1.3 65.0 + - - +
163A ILE* 4.0 14.4 - - + -
201A PHE* 4.0 13.2 - - + -
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Residues in contact with ALA 139 (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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106A PHE* 3.7 10.9 - - - -
131A LEU* 3.4 4.0 - - - +
132A VAL* 2.8 46.5 + - + +
134A LYS* 4.4 20.6 - - + -
137A LYS* 4.8 1.8 - - + +
138A LEU* 1.3 77.7 - - - +
140A VAL* 1.3 66.4 + - - +
141A VAL* 4.0 2.9 - - + -
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Residues in contact with VAL 140 (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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106A PHE* 3.9 21.3 - - + -
112A PHE* 4.0 21.5 - - + -
115A GLU* 3.5 33.2 + - + +
116A PHE* 3.8 20.2 - - + +
119A ALA* 3.5 30.0 - - + +
130A TRP 3.2 10.8 - - - +
131A LEU* 4.8 0.4 - - + -
139A ALA* 1.3 76.1 - - - +
141A VAL* 1.3 70.0 + - - +
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Residues in contact with VAL 141 (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 ALA* 5.1 1.6 - - - -
129A ALA* 3.5 1.4 - - - +
130A TRP* 2.6 45.5 + - + -
132A VAL* 3.8 33.0 - - + -
134A LYS* 4.4 22.4 - - - +
139A ALA* 4.7 2.5 - - + -
140A VAL* 1.3 85.3 - - - +
142A SER* 1.3 58.2 + - - +
149A PRO* 4.7 2.2 - - + -
158A ALA* 3.9 27.8 - - + -
159A SER 4.8 0.7 - - - +
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Residues in contact with SER 142 (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 ALA* 4.3 21.6 + - - +
123A ARG* 3.0 31.1 + - - +
128A TRP 3.1 15.9 - - - -
129A ALA* 4.3 3.6 - - - -
130A TRP* 4.2 1.1 - - - -
141A VAL* 1.3 75.4 - - - +
143A THR* 1.3 69.4 + - - +
156A SER 4.7 2.4 - - - +
157A GLY 5.4 1.2 - - - +
158A ALA* 4.2 8.0 - - - +
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Residues in contact with THR 143 (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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123A ARG* 3.3 12.1 + - - +
127A GLY* 3.2 3.3 - - - -
128A TRP* 3.0 32.5 + - - +
130A TRP* 3.0 22.4 + - + +
142A SER* 1.3 80.6 - - - +
144A ALA* 1.3 60.8 + - - +
147A ASP* 2.7 34.8 + - - +
149A PRO 4.1 6.5 - - - -
156A SER* 4.0 20.9 - - - +
158A ALA* 4.0 19.3 - - + -
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Residues in contact with ALA 144 (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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123A ARG* 3.6 20.7 - - - +
126A SER 3.7 4.5 - - - +
143A THR* 1.3 74.1 - - - +
145A ASN* 1.3 80.5 + - - +
146A GLN 3.1 0.5 + - - -
147A ASP* 2.9 33.7 + - - +
156A SER 5.0 2.2 + - - -
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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