Contacts of the strand formed by residues 136 - 146 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128F GLN* 2.8 47.8 + - - +
129F THR 3.6 7.8 + - - +
130F SER* 3.7 20.0 - - - -
134F GLY 3.4 8.0 + - - +
135F THR* 1.3 81.7 - - - +
137F VAL* 1.3 63.8 + - - +
138F GLN* 5.1 3.2 + - - +
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Residues in contact with VAL 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F THR* 2.9 35.6 + - + +
130F SER* 4.8 1.6 - - - -
131F LEU* 4.8 7.2 - - + +
135F THR* 4.4 8.7 - - + +
136F ARG* 1.3 76.5 - - - +
138F GLN* 1.4 66.5 + - + +
186F PRO* 3.3 30.6 - - + +
187F TYR 4.0 13.2 - - - +
188F ILE* 4.1 20.2 - - + -
189F PRO* 6.2 1.6 - - + -
194F LEU* 4.8 4.5 - - + -
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Residues in contact with GLN 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F GLN* 4.0 0.9 - - - -
129F THR* 3.4 26.8 + - - +
136F ARG* 5.1 4.9 + - - +
137F VAL* 1.4 87.1 - - + +
139F GLU* 1.3 61.0 + - - +
140F GLU* 3.4 22.0 - - + +
186F PRO* 5.4 8.3 - - + -
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Residues in contact with GLU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F HIS* 4.6 8.1 - - + -
127F LEU 3.4 7.9 - - - +
128F GLN* 4.5 16.6 - - + +
136F ARG* 5.5 3.1 - - - +
138F GLN* 1.3 76.7 - - - +
140F GLU* 1.3 61.5 + - - +
141F PRO* 3.3 11.9 - - + +
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Residues in contact with GLU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F VAL 4.0 1.4 - - - +
126F HIS* 3.1 2.2 + - - -
127F LEU* 2.8 57.5 + - + +
129F THR* 4.6 4.2 + - - -
138F GLN* 3.4 18.5 - - + +
139F GLU* 1.3 85.1 + - - +
141F PRO* 1.4 66.1 - - - +
142F GLU 3.3 2.5 + - - +
143F LEU* 4.1 32.9 - - + +
152F VAL* 5.7 3.1 - - - +
179F TYR* 5.5 2.3 + - - -
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Residues in contact with PRO 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F VAL 3.6 6.6 - - - +
126F HIS* 3.4 27.9 - - + +
139F GLU 3.3 12.5 - - - +
140F GLU* 1.4 82.6 - - - +
142F GLU* 1.3 62.2 + - + +
201F LYS* 2.8 26.5 + - - +
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Residues in contact with GLU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F THR* 3.8 20.6 - - + +
125F VAL 3.4 4.3 - - - -
140F GLU* 4.8 0.9 - - - +
141F PRO* 1.3 89.2 - - + +
143F LEU* 1.4 63.3 + - - +
144F VAL* 3.3 16.8 + - - +
201F LYS* 3.6 15.0 - - - +
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Residues in contact with LEU 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F VAL 3.7 1.4 - - - +
124F THR* 3.3 2.4 - - - -
125F VAL* 2.8 55.5 + - + +
127F LEU* 4.3 15.3 - - + -
140F GLU* 4.1 29.1 + - + +
141F PRO 4.0 0.2 - - - -
142F GLU* 1.4 70.1 - - - +
144F VAL* 1.3 62.3 + - - +
145F PHE* 4.1 9.2 - - + -
152F VAL* 3.9 27.4 - - + -
156F LEU* 3.8 28.7 - - + -
223F ARG* 4.3 13.0 - - - +
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Residues in contact with VAL 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F VAL* 3.6 25.1 - - + -
123F VAL 3.4 4.9 - - - +
124F THR* 3.5 25.1 - - + +
142F GLU* 3.3 20.1 + - - +
143F LEU* 1.3 73.3 - - - +
145F PHE* 1.3 66.1 + - - +
151F ASP* 4.9 0.2 - - - +
223F ARG* 3.7 24.6 + - - -
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Residues in contact with PHE 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F VAL* 3.6 4.7 - - - -
123F VAL* 2.9 66.7 + - + +
125F VAL* 3.7 25.6 - - + -
143F LEU* 4.1 14.6 - - + -
144F VAL* 1.3 79.1 - - - +
146F THR* 1.3 70.0 + - - +
147F LEU* 5.3 3.6 - - + -
151F ASP* 3.6 25.4 - - + +
152F VAL* 4.4 15.7 - - + -
156F LEU* 3.7 37.0 - - + -
157F ASP* 4.3 15.3 - - - -
160F VAL* 4.1 16.6 - - + -
223F ARG* 5.3 0.2 - - - +
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Residues in contact with THR 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F GLY* 3.4 32.8 - - - +
121F GLN 3.6 5.8 - - - +
122F VAL* 4.1 15.3 - - + +
145F PHE* 1.3 77.7 - - - +
147F LEU* 1.3 65.3 + - - +
148F GLY 3.4 0.3 + - - -
149F ASP* 3.3 43.2 + - - +
150F CYS 4.5 1.0 + - - -
151F ASP* 3.1 8.0 + - - +
157F ASP* 3.9 4.0 - - - +
206F GLY* 5.8 0.2 - - - -
207F PRO* 5.8 2.8 - - + +
220F LEU* 5.4 5.2 - - - +
224F LYS* 3.4 14.2 + - - -
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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