Contacts of the helix formed by residues 110 - 121 (chain A) in PDB entry 1MD9
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 ARG 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A PRO 2.8 23.2 + - - -
108A SER* 3.8 15.1 + - - +
109A HIS* 1.3 102.4 + - - +
111A SER* 1.3 58.2 + - - +
112A SER* 3.3 4.3 - - - +
113A GLU* 3.0 16.5 + - - +
114A ILE* 2.6 35.6 + - - +
135A PHE* 3.6 62.4 - - - +
137A TYR* 4.1 3.8 + - - -
140A LEU* 3.5 11.0 - - + -
143A GLN* 5.5 2.0 - - - +
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Residues in contact with SER 111 (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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110A ARG* 1.3 78.1 - - - +
112A SER* 1.3 68.0 + - - +
115A THR* 2.8 33.3 + - - -
140A LEU* 3.1 12.4 - - - +
143A GLN* 3.2 37.7 + - - +
144A VAL* 4.4 7.6 - - - -
147A LYS* 4.0 17.6 + - - -
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Residues in contact with SER 112 (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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110A ARG* 3.3 3.0 - - - +
111A SER* 1.3 83.6 + - - +
113A GLU* 1.3 73.8 + - - +
115A THR* 4.2 1.9 - - - -
116A TYR* 3.4 18.2 + - - +
147A LYS* 4.4 11.4 - - - +
196A LEU* 5.5 5.7 - - - +
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Residues in contact with GLU 113 (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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108A SER 5.3 1.2 - - - +
109A HIS* 3.9 27.2 - - + -
110A ARG* 3.0 31.3 + - - +
112A SER* 1.3 84.9 - - - +
114A ILE* 1.3 55.5 + - - +
115A THR 3.2 0.2 - - - -
116A TYR* 3.0 6.0 + - - +
117A PHE* 2.7 61.3 + - + -
196A LEU* 5.5 10.5 - - + -
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Residues in contact with ILE 114 (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 VAL* 4.7 2.7 - - + -
81A GLN* 3.1 31.9 - - - +
105A ALA* 4.0 7.6 - - + -
109A HIS* 4.0 9.0 - - + -
110A ARG 2.6 31.4 + - - +
113A GLU* 1.3 71.6 - - - +
115A THR* 1.3 51.4 + - - +
117A PHE* 3.5 16.8 - - + +
118A CYS* 2.7 43.2 + - - -
126A TYR* 3.4 38.8 - - + +
140A LEU* 4.2 4.3 - - + -
144A VAL* 3.6 18.2 - - + -
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Residues in contact with THR 115 (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 2.8 25.5 + - - -
112A SER 4.2 2.9 - - - -
114A ILE* 1.3 72.2 - - - +
116A TYR* 1.3 54.1 + - - +
119A GLU* 2.6 53.7 + - - +
144A VAL* 3.8 19.6 - - - +
147A LYS* 3.3 38.4 - - + +
148A LEU* 3.6 22.8 - - + +
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Residues in contact with TYR 116 (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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112A SER 3.4 13.1 + - - +
113A GLU* 3.0 9.2 + - - +
115A THR* 1.3 81.0 - - - +
117A PHE* 1.3 79.7 + + - +
119A GLU* 4.4 7.0 - - + -
120A PHE* 2.8 81.8 + + + +
196A LEU* 3.6 42.8 - - + +
197A SER 3.5 25.3 + - - -
198A LYS* 6.1 0.2 - - - +
199A LEU* 5.1 1.1 - - + -
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Residues in contact with PHE 117 (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 VAL* 4.1 18.3 - - + +
103A VAL* 5.0 5.6 - - + +
105A ALA* 3.6 18.2 - - + -
109A HIS* 3.3 40.6 - + + -
113A GLU* 2.7 35.3 + - + -
114A ILE* 3.5 15.3 - - + +
116A TYR* 1.3 88.8 - + - +
118A CYS* 1.3 61.3 + - - +
120A PHE* 4.1 3.8 - - - +
121A ALA* 3.1 30.5 + - - +
189A LEU* 3.5 39.3 - - + -
196A LEU* 6.1 0.7 - - + -
197A SER* 4.7 14.1 - - - -
199A LEU* 5.2 5.6 - - + +
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Residues in contact with CYS 118 (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 VAL* 3.9 18.6 - - - -
114A ILE* 2.7 36.2 + - - +
117A PHE* 1.3 72.9 - - - +
119A GLU* 1.3 64.7 + - - +
122A GLU* 3.2 2.9 + - - -
123A ALA* 3.1 38.4 + - + +
126A TYR* 4.7 4.9 - - - -
144A VAL* 4.2 1.3 - - - -
148A LEU* 3.5 18.8 - - + -
151A LEU* 3.6 30.3 - - + -
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Residues in contact with GLU 119 (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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115A THR* 2.6 35.4 + - - +
116A TYR* 3.9 7.7 - - + +
118A CYS* 1.3 76.0 - - - +
120A PHE* 1.3 66.2 + - - +
122A GLU* 3.3 11.6 + - - +
147A LYS 5.6 0.3 - - - +
148A LEU* 3.7 25.7 - - + +
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Residues in contact with PHE 120 (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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116A TYR* 2.8 62.6 + + + +
117A PHE* 4.1 1.8 - - - +
119A GLU* 1.3 70.6 - - - +
121A ALA* 1.3 52.9 + - - +
122A GLU* 2.7 26.3 + - - +
197A SER 5.1 1.1 - - - -
198A LYS* 5.4 2.5 - - + -
199A LEU* 3.2 48.7 - - + -
393A TYR* 3.9 19.3 - + - -
394A LYS* 3.7 44.7 + - + -
395A ALA* 5.5 2.2 - - + -
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Residues in contact with ALA 121 (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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77A ARG* 2.9 47.9 + - + +
103A VAL* 4.2 12.1 - - + -
117A PHE 3.1 17.1 + - - +
120A PHE* 1.3 77.6 - - - +
122A GLU* 1.3 67.4 + - - +
123A ALA* 3.1 4.4 + - + +
187A LEU* 4.8 1.3 - - + -
199A LEU* 4.1 15.9 - - + -
393A TYR* 4.2 12.3 - - - -
394A LYS* 4.7 0.2 - - - -
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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