Contacts of the helix formed by residues 183 - 194 (chain A) in PDB entry 3MTG
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 GLN 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ILE 2.8 19.7 + - - +
155A THR* 3.7 24.4 - - + +
156A ALA 4.8 1.3 - - - +
181A SER* 3.2 18.5 + - - +
182A THR* 1.4 72.1 - - - +
184A ASN* 1.3 63.9 + - - +
185A GLU* 3.3 17.1 - - - +
186A VAL* 3.3 32.4 - - + +
187A ALA* 3.4 5.7 + - - +
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Residues in contact with ASN 184 (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 LYS* 3.7 17.5 - - - +
109A ASN* 2.8 46.8 + - - +
112A GLN* 3.8 4.7 - - - +
182A THR* 3.4 4.3 + - - -
183A GLN* 1.3 72.0 - - - +
185A GLU* 1.3 69.7 + - - +
187A ALA* 3.0 16.1 + - - +
188A ALA 3.1 0.9 + - - -
199A ALA 4.3 0.5 - - - +
200A TRP* 3.3 23.7 - - - +
201A LYS* 3.1 41.5 + - - +
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Residues in contact with GLU 185 (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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109A ASN* 4.0 0.9 - - - +
112A GLN* 3.7 24.5 + - - +
115A PHE* 3.4 42.2 - - + -
116A GLY* 3.3 18.8 - - - +
119A GLU* 5.2 3.0 - - + +
183A GLN* 3.9 16.1 - - - +
184A ASN* 1.3 90.7 + - - +
186A VAL* 1.4 62.8 + - + +
188A ALA* 3.3 13.5 + - - +
189A ALA 3.3 9.5 + - - -
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Residues in contact with VAL 186 (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 GLY* 4.2 4.3 - - - +
119A GLU* 4.2 16.8 - - + -
120A ILE* 4.1 18.2 - - + -
154A ILE* 3.7 21.1 - - + +
155A THR* 3.7 19.3 - - - +
156A ALA* 3.8 30.5 - - + +
159A ALA* 4.5 4.0 - - + -
183A GLN* 3.3 20.4 + - + +
185A GLU* 1.4 71.9 - - + +
187A ALA* 1.4 69.2 + - - +
188A ALA 3.1 1.9 + - - -
189A ALA* 3.1 3.0 + - - +
190A LEU* 2.9 28.8 + - + +
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Residues in contact with ALA 187 (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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107A VAL* 3.7 20.7 - - + +
109A ASN* 4.0 1.8 - - - +
154A ILE* 4.4 10.1 - - + -
182A THR* 4.6 3.4 - - + -
183A GLN 3.4 5.1 + - - +
184A ASN* 3.0 18.0 + - - +
186A VAL* 1.4 81.3 - - - +
188A ALA* 1.4 54.2 + - - +
190A LEU* 3.8 7.4 + - - -
191A ALA* 3.2 12.3 + - - +
197A VAL* 3.1 32.5 - - + +
199A ALA 4.0 11.0 - - - +
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Residues in contact with ALA 188 (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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107A VAL* 4.5 3.1 - - - -
109A ASN* 3.3 34.0 + - + +
112A GLN* 3.7 2.9 - - - +
113A ALA* 3.5 24.0 - - + +
184A ASN 3.1 5.1 + - - -
185A GLU 3.4 10.3 - - - +
186A VAL 3.1 0.4 - - - -
187A ALA* 1.4 73.9 - - - +
189A ALA* 1.4 59.0 + - - +
191A ALA* 3.0 7.9 + - - +
192A GLU* 2.9 30.5 + - - +
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Residues in contact with ALA 189 (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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113A ALA* 3.6 17.4 - - - +
116A GLY 3.7 3.4 - - - -
117A ARG* 2.9 59.7 + - + +
120A ILE* 3.7 8.3 - - + -
185A GLU 3.3 2.2 + - - +
186A VAL 3.1 7.5 + - - +
188A ALA* 1.4 77.4 - - - +
190A LEU* 1.4 50.5 + - - +
192A GLU* 3.6 4.8 + - - +
193A ALA* 2.9 26.2 + - - +
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Residues in contact with LEU 190 (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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120A ILE* 4.5 2.9 - - + -
154A ILE* 4.0 25.6 - - + -
159A ALA* 3.8 28.3 - - + +
162A ILE* 4.2 23.8 - - + -
163A GLU* 3.6 33.9 - - + +
186A VAL 2.9 21.1 + - - +
187A ALA* 3.8 5.8 - - - +
189A ALA* 1.4 73.2 - - - +
191A ALA* 1.3 61.8 + - - +
193A ALA* 3.1 6.8 + - - +
194A GLY 3.1 6.2 + - - -
195A VAL* 2.9 36.5 + - + +
197A VAL* 4.2 11.9 - - + -
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Residues in contact with ALA 191 (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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102A SER* 5.8 1.9 + - - -
105A PHE* 3.6 52.3 - - + -
107A VAL* 4.4 4.7 - - + -
187A ALA 3.2 12.7 + - - +
188A ALA* 3.0 9.5 + - - +
190A LEU* 1.3 76.7 - - - +
192A GLU* 1.3 58.1 + - - +
194A GLY* 3.2 19.1 + - - -
195A VAL 3.5 12.9 - - - +
197A VAL* 3.8 3.6 - - + +
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Residues in contact with GLU 192 (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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105A PHE* 5.8 0.8 - - - -
113A ALA* 3.8 23.3 - - + -
188A ALA 2.9 15.7 + - - +
189A ALA* 3.7 5.8 - - - +
191A ALA* 1.3 75.0 - - - +
193A ALA* 1.4 59.9 + - - +
194A GLY* 3.2 1.5 + - - -
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Residues in contact with ALA 193 (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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117A ARG* 3.5 16.4 - - - +
163A GLU* 3.7 11.9 - - - +
189A ALA 2.9 18.6 + - - +
190A LEU* 3.1 8.9 + - - +
192A GLU* 1.4 76.1 - - - +
194A GLY* 1.3 55.7 + - - +
195A VAL* 3.7 6.4 - - + +
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Residues in contact with GLY 194 (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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102A SER* 6.5 1.1 - - - -
104A ASN 5.4 0.9 - - - +
190A LEU 3.1 1.2 + - - -
191A ALA 3.2 10.7 + - - -
192A GLU 3.2 1.6 - - - -
193A ALA* 1.3 78.3 - - - +
195A VAL* 1.4 65.4 + - - +
196A ALA* 3.6 2.9 + - - +
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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