Contacts of the strand formed by residues 142 - 153 (chain G) in PDB entry 5IXM
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 TRP 142 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137G TYR* 3.7 27.6 - + + -
138G ALA* 3.6 0.3 - - - -
139G ASN* 2.9 68.9 + - - +
140G GLU 3.7 0.6 - - - -
141G ASN* 1.3 85.9 - - + +
143G ASN* 1.3 84.0 + - - +
144G ALA* 3.6 27.4 - - + -
171G MET* 3.7 20.2 - - + -
172G ASN 3.1 15.9 - - - +
173G TYR* 4.1 15.9 - + + -
174G TYR* 4.8 1.6 - - - -
30H ARG* 5.6 0.2 - - - -
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Residues in contact with ASN 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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137G TYR 3.2 15.5 - - - +
138G ALA* 3.6 14.7 - - + +
139G ASN 5.6 0.2 + - - -
142G TRP* 1.3 86.1 - - - +
144G ALA* 1.3 62.7 + - - +
145G THR* 4.9 5.7 + - - +
170G ASP 4.7 1.4 - - - +
171G MET* 3.3 2.8 - - - -
172G ASN* 2.9 67.1 + - - +
174G TYR* 3.8 16.0 + - - -
25H TYR 5.7 0.6 + - - -
30H ARG* 4.2 11.7 - - - +
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Residues in contact with ALA 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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136G GLY* 3.2 0.4 - - - -
137G TYR* 2.9 35.1 + - + +
142G TRP* 3.6 22.3 - - + -
143G ASN* 1.3 75.3 - - - +
145G THR* 1.3 68.1 + - - +
169G LEU* 4.7 5.6 - - + -
170G ASP 3.2 5.6 - - - -
171G MET* 3.7 19.7 - - + -
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Residues in contact with THR 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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100G ARG* 5.9 2.4 - - - -
134G THR* 3.7 21.8 - - + -
135G ALA 3.8 6.7 - - - +
136G GLY* 4.0 4.1 - - - -
137G TYR 5.0 0.9 + - - -
143G ASN* 4.9 6.2 + - - +
144G ALA* 1.3 81.1 + - - +
146G LEU* 1.3 61.8 + - - +
147G SER* 3.5 20.3 + - - +
168G GLN 3.5 2.1 - - - +
169G LEU* 3.3 9.8 - - - +
170G ASP* 2.8 50.3 + - + +
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Residues in contact with LEU 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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133G PHE 4.6 0.3 - - - -
134G THR* 3.5 0.5 - - - -
135G ALA* 2.9 41.5 + - + +
145G THR* 1.3 71.7 - - - +
147G SER* 1.3 65.8 + - - +
167G PRO* 4.1 24.5 - - + -
168G GLN 3.6 11.9 - - - +
169G LEU* 4.2 22.0 - - + +
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Residues in contact with SER 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G PHE 3.1 9.6 - - - -
134G THR* 3.1 18.1 + - - -
145G THR* 3.5 14.6 - - - +
146G LEU* 1.3 79.8 + - - +
148G SER* 1.3 59.4 + - - +
149G LYS* 4.2 23.1 - - - -
165G ALA 4.0 0.3 - - - +
167G PRO* 3.5 8.9 - - - +
168G GLN* 2.9 42.9 + - - +
170G ASP* 5.4 3.3 + - - -
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Residues in contact with SER 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G GLN 3.6 1.6 - - - +
132G ILE* 3.2 6.1 - - - -
133G PHE* 2.9 50.1 + - - +
147G SER* 1.3 73.9 - - - +
149G LYS* 1.3 65.4 + - - +
150G GLN* 4.1 7.9 + - - +
165G ALA 3.5 8.0 + - - -
166G GLN* 5.1 9.8 - - - +
167G PRO* 5.1 3.8 - - - -
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Residues in contact with LYS 149 (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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131G GLN 3.8 2.5 - - - -
132G ILE* 3.9 28.3 - - + -
134G THR* 5.7 0.7 - - - -
147G SER* 4.4 16.4 - - - -
148G SER* 1.3 77.4 - - - +
150G GLN* 1.3 60.6 + - - +
151G PHE* 4.2 7.4 - - + -
164G ARG* 3.4 7.3 - - - +
165G ALA* 2.9 44.0 + - + +
168G GLN* 3.2 41.1 + - - +
170G ASP* 5.0 1.8 + - - -
114H LEU* 4.0 17.5 - - + -
117H GLU* 4.5 17.9 - - + +
118H ALA* 5.6 6.1 - - - +
121H GLU* 5.1 10.3 - - - +
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Residues in contact with GLN 150 (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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105G TYR* 6.0 0.5 - - - -
131G GLN* 2.9 57.5 + - + +
148G SER* 5.1 8.3 + - - +
149G LYS* 1.3 75.9 - - - +
151G PHE* 1.3 76.5 + - - +
164G ARG* 3.4 41.3 - - + +
166G GLN* 4.9 6.9 + - - +
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Residues in contact with PHE 151 (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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128G TYR* 4.1 9.4 - + + -
129G ALA 3.4 4.7 - - - +
130G THR* 3.8 36.8 - - + -
131G GLN* 4.8 2.7 - - - -
132G ILE* 4.5 10.1 - - + -
149G LYS* 4.2 4.5 - - + -
150G GLN* 1.3 94.7 + - - +
152G GLN* 1.3 60.5 + - - +
153G VAL* 3.7 8.8 + - + +
159G ASN* 3.3 13.9 - - - +
162G ALA* 4.9 6.6 - - + +
163G TYR 4.1 11.4 - - - -
164G ARG* 4.2 14.0 + - - +
113H ALA* 3.6 31.0 - - + -
114H LEU* 3.5 42.2 - - + -
117H GLU* 4.2 18.8 - - + -
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Residues in contact with GLN 152 (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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107G ARG* 3.4 20.0 - - - +
108G VAL* 2.8 60.6 + - - +
109G SER 5.0 0.6 - - - -
110G ASP* 4.7 6.3 + - - +
128G TYR* 3.2 3.3 - - - -
129G ALA* 2.9 37.8 + - + +
131G GLN* 3.9 12.2 - - - +
151G PHE* 1.3 70.0 - - - +
153G VAL* 1.3 63.5 + - - +
154G PHE* 3.3 9.4 - - + -
159G ASN* 3.8 10.8 - - - +
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Residues in contact with VAL 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G PRO* 5.7 1.4 - - - +
127G GLY 3.7 8.3 - - - +
128G TYR* 3.7 10.5 - - + -
151G PHE* 4.6 7.6 - - + +
152G GLN* 1.3 73.9 - - - +
154G PHE* 1.3 63.1 + - - +
155G THR* 3.1 20.9 + - + +
158G GLY* 3.6 21.3 - - - +
159G ASN* 3.4 26.6 + - - +
162G ALA* 3.6 29.8 - - + -
110H PRO* 3.5 32.3 - - + +
111H LEU* 4.6 1.6 - - + -
113H ALA* 5.2 1.3 - - + -
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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