Contacts of the helix formed by residues 137 - 147 (chain A) in PDB entry 1MDF
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLN* 3.9 22.7 - - + -
83A PRO* 5.9 0.4 - - + -
107A PRO* 2.6 42.4 + - + +
110A ARG* 4.2 2.3 + - - -
126A TYR* 5.0 0.3 + - - -
128A ILE* 3.2 17.1 - - + +
129A PRO* 3.3 41.1 - - + +
130A ASP 3.1 6.5 + - - -
131A ALA* 4.1 0.9 - - - -
132A TYR* 3.5 32.1 + - + -
135A PHE* 3.3 44.5 - + - +
136A ASP* 1.3 68.4 - - - +
138A ARG* 1.3 60.3 + - - +
139A SER 3.2 1.8 - - - -
140A LEU* 3.1 18.7 + - + +
141A ALA* 2.8 22.9 + - - +
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Residues in contact with ARG 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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128A ILE* 3.9 6.5 - - + -
129A PRO 4.5 0.7 - - - +
130A ASP* 3.0 35.6 + - - +
131A ALA* 4.9 3.6 - - - +
136A ASP* 2.9 37.3 + - - +
137A TYR* 1.3 75.1 - - - +
139A SER* 1.3 61.4 + - - +
141A ALA* 3.1 5.5 + - - +
142A ARG* 2.9 42.6 + - - +
156A VAL* 4.4 20.0 - - + -
159A GLU* 3.1 29.8 + - - +
160A ALA 4.8 0.4 - - - +
161A GLU* 3.0 45.0 + - - +
163A PHE* 3.8 13.5 - - + -
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Residues in contact with SER 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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135A PHE* 5.1 3.8 - - - -
136A ASP* 2.8 33.9 + - - +
138A ARG* 1.3 74.4 - - - +
140A LEU* 1.3 62.7 + - - +
142A ARG* 3.2 21.1 + - - +
143A GLN* 3.0 32.8 + - - +
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Residues in contact with LEU 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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81A GLN* 4.0 1.8 - - - +
109A HIS 3.7 19.7 - - - +
110A ARG* 3.5 5.8 - - + +
111A SER* 3.1 42.6 - - - +
114A ILE* 4.5 0.4 - - + -
126A TYR* 3.6 21.8 - - - +
135A PHE* 3.7 34.3 - - + -
137A TYR* 3.1 20.1 + - + +
139A SER* 1.3 80.7 + - - +
141A ALA* 1.3 57.2 + - - +
143A GLN* 3.1 15.3 + - - +
144A VAL* 3.0 28.0 + - + +
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Residues in contact with ALA 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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126A TYR* 4.0 21.1 - - + -
128A ILE* 3.9 15.9 - - + -
137A TYR 2.8 13.1 + - - +
138A ARG* 3.3 11.7 - - - +
140A LEU* 1.3 75.3 - - - +
142A ARG* 1.3 64.5 + - - +
144A VAL* 3.2 3.5 + - - +
145A GLN* 3.0 28.9 + - - +
154A ILE* 4.1 18.5 - - + +
163A PHE* 4.2 6.1 - - + -
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Residues in contact with ARG 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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136A ASP* 5.8 0.4 - - - -
138A ARG* 2.9 44.3 + - - +
139A SER* 3.2 19.1 - - - +
140A LEU 3.3 0.4 - - - -
141A ALA* 1.3 75.5 - - - +
143A GLN* 1.3 63.3 + - + +
145A GLN* 3.3 9.2 + - - +
146A SER* 3.1 23.4 + - - -
161A GLU* 2.7 28.5 + - - +
162A GLU* 2.5 44.4 + - - +
163A PHE* 3.9 11.5 - - + -
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Residues in contact with GLN 143 (chain A).
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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111A SER* 4.2 22.0 + - - -
135A PHE* 5.2 5.5 - - - -
139A SER* 3.0 16.2 + - - +
140A LEU* 3.1 33.2 + - - +
142A ARG* 1.3 76.5 - - + +
144A VAL* 1.3 61.1 + - - +
146A SER* 2.9 20.4 + - - -
147A LYS* 3.4 17.7 + - - +
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Residues in contact with VAL 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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111A SER* 4.5 2.0 - - - -
114A ILE* 3.7 36.3 - - + -
115A THR* 4.1 19.7 - - - +
118A CYS* 4.8 0.9 - - - -
126A TYR* 4.3 4.9 - - + -
140A LEU* 3.0 27.4 + - + +
141A ALA* 3.5 9.0 - - - +
142A ARG 3.1 0.4 - - - -
143A GLN* 1.3 76.6 - - - +
145A GLN* 1.3 53.6 + - - +
147A LYS* 3.1 4.7 + - - +
148A LEU* 2.7 42.9 + - + +
151A LEU* 3.4 30.5 - - + -
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Residues in contact with GLN 145 (chain A).
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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141A ALA 3.0 18.1 + - - +
142A ARG* 3.3 9.6 + - - +
144A VAL* 1.3 73.5 - - - +
146A SER* 1.3 63.2 + - - +
148A LEU 3.9 8.5 - - - +
149A PRO* 2.7 36.2 + - + +
151A LEU* 3.0 28.7 + - + +
152A LYS* 4.5 6.7 + - - +
154A ILE* 3.8 27.5 - - + +
163A PHE* 3.7 19.0 - - - -
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Residues in contact with SER 146 (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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142A ARG 3.1 12.6 + - - -
143A GLN* 2.9 25.6 + - - -
145A GLN* 1.3 77.5 - - - +
147A LYS* 1.3 63.6 + - - +
148A LEU 3.5 0.3 + - - -
149A PRO* 3.8 7.8 - - - +
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Residues in contact with LYS 147 (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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111A SER* 4.1 20.2 + - - -
112A SER* 4.1 15.2 - - - +
115A THR* 3.6 33.4 + - + +
119A GLU* 5.2 0.9 - - - +
143A GLN* 3.4 13.2 + - - +
144A VAL 3.1 7.0 + - - +
145A GLN 3.1 0.4 - - - -
146A SER* 1.3 81.4 + - - +
148A LEU* 1.3 68.4 + - - +
149A PRO* 3.8 3.0 - - - +
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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