Contacts of the strand formed by residues 136 - 146 (chain G) in PDB entry 5MGX
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 136 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128G GLN* 5.7 4.7 - - - -
129G THR 3.6 7.6 - - - +
130G SER* 4.1 8.7 - - - +
134G GLY 3.4 9.1 + - - +
135G THR* 1.3 81.7 - - - +
137G VAL* 1.3 62.9 + - - +
138G GLN* 5.0 3.1 - - - +
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Residues in contact with VAL 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G THR* 2.9 31.3 + - + +
131G LEU* 4.0 27.1 - - + -
135G THR* 4.4 1.3 - - + +
136G ARG* 1.3 77.4 - - - +
138G GLN* 1.3 72.8 + - + +
186G PRO 4.1 7.2 - - - +
187G TYR 3.9 13.0 - - - +
188G ILE* 3.7 40.4 - - + -
194G LEU* 4.8 0.4 - - + -
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Residues in contact with GLN 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G LEU 4.3 0.4 - - - +
128G GLN* 3.9 2.3 - - - -
129G THR* 3.4 32.3 + - - +
136G ARG* 3.9 3.5 - - - +
137G VAL* 1.3 93.0 - - + +
139G GLU* 1.3 62.2 + - - +
140G GLU* 3.4 40.9 + - - +
179G TYR* 5.0 9.5 + - - -
186G PRO* 5.3 14.9 + - - +
188G ILE* 5.6 2.6 - - - +
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Residues in contact with GLU 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G HIS* 2.8 31.5 + - - -
127G LEU 3.5 3.4 - - - +
128G GLN* 3.6 33.8 - - + +
138G GLN* 1.3 77.1 - - - +
140G GLU* 1.3 65.1 + - - +
141G PRO* 3.9 19.7 - - - +
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Residues in contact with GLU 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G VAL 3.7 2.3 - - - +
126G HIS* 3.3 2.0 - - - -
127G LEU* 2.8 55.6 + - + +
129G THR* 4.8 1.2 + - - -
138G GLN* 3.4 41.1 + - - +
139G GLU* 1.3 77.9 - - - +
141G PRO* 1.4 67.4 - - - +
142G GLU 3.3 1.7 + - - +
143G LEU* 3.6 40.2 - - + +
152G VAL* 5.8 2.0 - - - +
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Residues in contact with PRO 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G VAL 3.2 9.7 - - - +
126G HIS* 3.7 27.6 - - + +
139G GLU* 3.9 14.8 - - - +
140G GLU* 1.4 84.5 - - - +
142G GLU* 1.3 65.2 + - + +
201G LYS* 2.8 30.0 + - - +
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Residues in contact with GLU 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G THR* 4.1 16.2 - - + -
125G VAL 3.6 2.0 - - - -
140G GLU* 3.3 2.2 - - - -
141G PRO* 1.3 93.3 - - + +
143G LEU* 1.4 61.9 + - - +
144G VAL* 3.5 11.2 + - + +
201G LYS* 3.7 14.1 - - - +
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Residues in contact with LEU 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G VAL 3.8 1.2 - - - +
124G THR* 3.3 3.3 - - - -
125G VAL* 2.8 53.4 + - + +
127G LEU* 4.2 14.8 - - + -
140G GLU* 3.6 35.1 + - + +
142G GLU* 1.4 70.9 - - - +
144G VAL* 1.3 61.4 + - - +
145G PHE* 3.8 13.0 + - + -
152G VAL* 3.9 26.5 - - + -
156G LEU* 3.8 28.7 - - + -
223G ARG* 4.3 12.8 - - - +
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Residues in contact with VAL 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G VAL* 3.6 25.8 - - + -
123G VAL 3.5 4.5 - - - +
124G THR* 3.5 25.6 - - + +
142G GLU* 3.5 13.8 + - + +
143G LEU* 1.3 75.6 - - - +
145G PHE* 1.3 64.8 + - - +
223G ARG* 3.8 23.9 + - - -
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Residues in contact with PHE 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G VAL* 3.7 4.8 - - - -
123G VAL* 2.9 55.9 + - + +
125G VAL* 3.7 29.6 - - + -
143G LEU* 3.8 26.9 - - + -
144G VAL* 1.3 75.7 - - - +
146G THR* 1.3 70.3 + - - +
147G LEU* 4.2 13.2 - - + -
151G ASP* 3.6 25.6 - - + +
152G VAL* 4.3 9.2 - - + -
156G LEU* 3.9 33.4 - - + -
157G ASP* 4.7 10.1 - - - -
160G VAL* 4.1 14.6 - - + -
223G ARG* 5.3 0.2 - - - +
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Residues in contact with THR 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G GLY* 3.4 32.5 - - - +
121G GLN 3.6 4.9 - - - +
122G VAL* 4.0 15.1 - - + +
145G PHE* 1.3 77.1 - - - +
147G LEU* 1.3 67.0 + - - +
148G GLY 3.4 0.3 + - - -
149G ASP* 3.3 42.3 + - - +
150G CYS 4.5 1.0 + - - -
151G ASP* 3.1 7.8 + - - +
157G ASP* 3.9 3.8 - - - +
207G PRO* 5.8 2.6 - - + +
220G LEU* 5.4 4.7 - - - +
224G LYS* 3.4 14.0 + - - -
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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