Contacts of the helix formed by residues 116 - 130 (chain B) in PDB entry 3MEU
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 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B GLY* 1.3 67.7 + - - +
118B VAL* 3.3 6.0 - - - +
119B LEU* 3.3 20.0 + - - +
120B MSE 3.1 29.5 + - + +
2D 2MR 4.4 31.9 - - - +
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Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ARG* 1.3 77.7 - - - +
118B VAL* 1.3 62.3 + - - +
120B MSE 3.3 7.4 + - - +
121B THR* 3.1 26.3 + - - -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ARG 3.3 3.4 - - - +
117B GLY* 1.3 73.7 - - - +
119B LEU* 1.3 66.1 + - - +
121B THR* 3.1 9.7 + - - -
122B LEU* 3.0 37.5 + - + +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ARG* 3.3 21.7 + - + +
117B GLY 3.3 0.2 - - - -
118B VAL* 1.3 78.5 - - - +
120B MSE 1.3 66.6 + - - +
122B LEU* 3.2 11.5 + - + +
123B LEU* 3.0 44.1 + - + +
195B ILE* 3.7 25.8 - - + +
196B ASP* 3.7 29.6 - - + +
242B THR* 3.9 17.9 - - + -
2D 2MR 5.1 9.4 - - + -
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Residues in contact with MSE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ARG* 3.1 15.6 + - + +
117B GLY* 3.8 8.3 - - - +
118B VAL 3.3 0.2 - - - -
119B LEU* 1.3 78.0 - - + +
121B THR* 1.3 62.4 + - - +
123B LEU* 3.3 21.0 + - + +
124B GLN* 2.9 29.1 + - + +
237B LEU* 6.4 0.4 - - + -
240B GLN* 3.8 66.2 - - - +
241B THR 4.2 11.2 - - - +
242B THR* 5.0 3.1 - - - -
2D 2MR 5.0 10.1 - - - +
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLY 3.1 15.3 + - - -
118B VAL* 3.1 13.7 + - - -
120B MSE 1.3 76.3 - - - +
122B LEU* 1.3 63.5 + - + +
124B GLN* 3.9 5.3 + - - +
125B GLN* 2.9 38.0 + - + +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B VAL* 3.0 31.5 + - + +
119B LEU* 3.2 11.6 + - + +
121B THR* 1.3 80.3 - - + +
123B LEU* 1.3 60.5 + - + +
125B GLN* 3.3 9.4 + - + +
126B SER* 2.8 29.7 + - - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LEU* 3.0 28.0 + - + +
120B MSE 3.7 17.9 - - + +
122B LEU* 1.3 81.2 - - + +
124B GLN* 1.3 61.9 + - - +
126B SER* 3.2 3.3 + - - -
127B ALA 3.1 9.9 + - - -
177B LEU* 3.6 29.8 - - + -
195B ILE* 3.9 22.4 - - + -
237B LEU* 4.4 6.7 - - + -
241B THR 4.1 12.1 - - - +
242B THR* 3.7 27.8 - - + -
283B TYR* 2.7 31.3 + - + +
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Residues in contact with GLN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B MSE 2.9 20.7 + - + +
121B THR* 3.9 4.6 + - - +
123B LEU* 1.3 76.9 - - - +
125B GLN* 1.3 86.8 + - - +
127B ALA* 3.2 10.1 + - + +
128B MSE 3.0 46.9 + - - +
283B TYR* 5.3 0.9 - - - -
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 2.9 27.0 + - + +
122B LEU* 3.3 11.9 + - + +
124B GLN* 1.3 95.2 + - - +
126B SER* 1.3 56.7 + - - +
128B MSE 3.2 14.5 + - - +
129B THR* 2.8 61.4 + - + +
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LEU 2.8 17.2 + - - -
123B LEU* 3.5 8.3 - - - -
124B GLN 3.2 0.2 - - - -
125B GLN* 1.3 75.4 - - - +
127B ALA* 1.3 64.1 + - - +
129B THR* 3.6 6.0 + - - -
130B LEU 3.4 8.0 + - - -
161B LYS* 4.4 15.1 - - - +
282B ARG* 2.9 50.3 + - - +
283B TYR* 3.5 8.2 + - - -
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU 3.1 6.4 + - - +
124B GLN* 3.2 14.6 + - + +
126B SER* 1.3 78.3 - - - +
128B MSE 1.3 56.9 + - - +
130B LEU* 3.5 7.6 + - - +
217B LYS* 3.0 23.3 + - - -
280B ALA* 3.5 31.6 - - + +
282B ARG* 4.1 13.7 + - + +
283B TYR* 3.7 19.5 + - + -
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Residues in contact with MSE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLN* 3.0 38.9 + - - +
125B GLN* 3.4 28.3 - - - +
127B ALA* 1.3 78.0 - - + +
129B THR* 1.3 61.0 + - + +
130B LEU 3.9 0.2 - - - +
217B LYS* 2.7 22.9 + - - +
257B GLN* 5.5 15.5 - - + +
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLN* 2.8 42.3 + - + +
126B SER* 3.6 8.8 + - - -
128B MSE 1.3 78.1 - - + +
130B LEU* 1.3 66.2 + - - +
131B PRO* 3.1 10.6 - - - +
282B ARG* 4.4 3.7 + - - -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B SER 3.4 6.5 + - - +
127B ALA 3.6 12.6 - - - +
128B MSE 3.3 1.9 - - - +
129B THR* 1.3 74.1 - - - +
131B PRO* 1.3 72.3 - - + +
132B LEU* 3.7 0.5 + - - +
214B PRO* 3.5 21.8 - - + +
215B GLN* 3.5 22.2 - - - +
216B TRP 3.7 6.7 - - - +
217B LYS* 2.8 57.5 + - + +
281B GLN 4.7 0.7 - - - -
282B ARG* 3.6 59.6 - - + +
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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