Contacts of the helix formed by residues 119 - 140 (chain B) in PDB entry 1GPU
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 GLY 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER 4.8 0.4 + - - -
118B LEU* 1.3 72.6 - - - +
120B GLN* 1.3 61.0 + - - +
121B GLY 3.5 1.8 - - - -
122B ILE* 3.3 13.2 - - - +
123B SER* 2.8 23.7 + - - -
159B CYS* 3.3 35.4 - - - +
162B GLU* 4.3 0.9 - - - -
164B ILE* 3.4 19.1 - - - +
165B SER* 4.6 0.2 - - - -
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A TYR* 2.8 22.2 + - - +
114B THR 5.0 2.5 - - - +
115B THR* 5.2 1.3 - - + -
117B PRO* 3.1 22.1 + - + +
118B LEU 3.3 0.2 - - - -
119B GLY* 1.3 75.8 - - - +
121B GLY* 1.3 54.6 + - - +
123B SER* 3.1 4.8 + - - -
124B ASN* 2.8 46.7 + - - +
164B ILE* 3.7 4.7 - - - +
419B HIS* 3.1 22.0 + - - -
423B ALA* 3.6 13.3 - - - +
426B ASN* 5.2 1.0 - - - +
451B GLY 3.5 4.8 - - - -
452B ALA* 3.5 29.6 - - - +
455B LEU* 3.5 30.7 - - + +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 3.4 28.9 - - - +
66B SER* 3.3 12.2 + - - +
115B THR* 3.7 15.5 - - - +
117B PRO 4.8 0.4 + - - -
119B GLY 4.8 0.2 - - - +
120B GLN* 1.3 77.4 - - - +
122B ILE* 1.3 63.4 + - - +
124B ASN* 3.1 11.6 + - - +
125B ALA* 2.9 19.2 + - - +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER* 2.9 14.9 + - - +
119B GLY* 3.3 18.6 - - - +
121B GLY* 1.3 71.5 - - - +
123B SER* 1.3 65.1 + - - +
125B ALA* 3.3 4.8 + - + +
126B VAL* 3.1 27.9 + - + +
153B VAL* 3.9 28.3 - - + -
155B LEU* 4.3 23.1 - - + -
159B CYS* 4.6 0.9 - - + -
165B SER* 3.7 22.7 - - - +
168B ALA* 5.6 0.9 - - + -
169B SER* 4.5 14.8 - - - +
180B LEU* 5.1 1.8 - - + -
182B ALA* 4.3 17.7 - - + -
207B TYR* 5.1 1.6 - - + +
212B TRP* 4.5 15.3 - - + -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLY 2.8 17.1 + - - -
120B GLN 3.1 6.0 + - - -
122B ILE* 1.3 77.6 - - - +
124B ASN* 1.3 63.2 + - - +
126B VAL* 3.2 13.3 + - - +
127B GLY 3.3 8.1 + - - -
164B ILE* 3.5 17.5 + - - +
165B SER* 4.1 1.6 - - - -
168B ALA* 3.4 28.7 - - - +
420B ALA 4.9 1.6 - - - -
423B ALA* 3.4 27.1 - - - -
424B ILE* 3.5 9.9 - - - +
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Residues in contact with ASN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 3.5 43.6 - - + +
114B THR 4.3 5.5 - - - +
120B GLN* 2.8 37.7 + - - +
121B GLY* 3.3 8.0 + - - +
123B SER* 1.3 71.9 - - - +
125B ALA* 1.3 59.6 + - - +
127B GLY 3.0 3.5 + - - -
128B MET* 2.9 26.3 + - + +
423B ALA* 2.9 34.1 + - - +
426B ASN* 3.8 13.1 - - - +
427B GLY* 3.3 11.5 - - - -
455B LEU* 5.6 1.1 - - - +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 4.4 5.4 - - + +
121B GLY 2.9 11.0 + - - +
122B ILE 3.4 8.5 - - - +
124B ASN* 1.3 75.9 - - - +
126B VAL* 1.3 65.1 + - - +
128B MET* 3.1 10.4 + - - +
129B ALA* 2.9 22.0 + - - +
151B THR* 3.5 18.6 - - + +
153B VAL* 3.0 37.2 - - + -
180B LEU* 4.0 4.9 - - + +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 3.1 20.4 + - + +
123B SER 3.2 8.5 + - - +
125B ALA* 1.3 76.1 - - - +
127B GLY* 1.3 61.0 + - - +
129B ALA* 3.3 3.0 + - - +
130B MET* 3.0 44.4 + - - +
168B ALA* 3.8 28.5 - - + +
169B SER* 4.9 0.4 - - - +
171B LEU 5.4 0.9 - - - -
172B ALA* 3.9 28.5 - - + +
175B LEU* 5.4 0.2 - - + -
177B LEU* 3.9 5.1 - - + +
180B LEU* 3.9 17.0 - - + -
212B TRP* 5.2 1.1 - - + -
424B ILE* 4.0 13.0 - - + -
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B SER 3.3 4.4 + - - -
124B ASN 3.0 9.0 + - - -
126B VAL* 1.3 78.6 - - - +
128B MET* 1.3 59.3 + - - +
130B MET* 3.2 2.6 + - - +
131B ALA* 2.9 25.1 + - - +
424B ILE* 3.5 34.3 - - - +
428B ILE* 3.3 18.1 - - - +
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 4.3 24.7 - - - -
64B VAL* 3.6 25.4 - - + -
112B GLU* 3.6 26.5 - - + +
113B VAL* 3.5 32.8 - - + -
124B ASN* 2.9 17.1 + - + +
125B ALA* 3.1 11.2 + - - +
127B GLY* 1.3 76.1 - - - +
129B ALA* 1.3 57.7 + - - +
131B ALA* 3.3 5.9 + - - +
132B GLN* 3.0 27.5 + - - +
149B ASN* 5.7 0.2 + - - -
151B THR* 3.9 16.3 + - + +
427B GLY* 3.4 16.4 - - - +
430B ALA* 4.1 9.2 - - + -
431B PHE* 3.7 9.7 - - + +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ALA 2.9 16.3 + - - +
126B VAL 3.7 4.7 - - - +
127B GLY 3.2 0.2 - - - -
128B MET* 1.3 73.8 - - - +
130B MET* 1.3 64.9 + - - +
132B GLN* 3.4 8.1 + - - +
133B ALA* 3.0 23.6 + - - +
151B THR* 3.7 14.3 + - - +
177B LEU* 4.2 17.5 - - + +
179B ASN* 5.1 4.9 - - + +
180B LEU* 4.0 27.4 - - + +
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Residues in contact with MET 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 3.0 26.5 + - - +
127B GLY* 3.2 5.6 + - - +
129B ALA* 1.3 78.6 - - - +
131B ALA* 1.3 61.2 + - - +
133B ALA* 3.3 4.4 + - - +
134B ASN* 3.0 21.0 + - - +
171B LEU* 5.0 1.1 - - + -
175B LEU* 3.7 28.7 - - + -
177B LEU* 3.7 16.4 - - + -
397B PHE* 3.6 26.3 - - + -
412B ILE* 3.5 45.1 - - + -
414B TYR* 4.8 0.7 - - + -
424B ILE* 3.6 29.8 - - + -
428B ILE* 4.5 5.6 - - + -
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Residues in contact with ALA 131 (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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127B GLY 2.9 16.8 + - - +
128B MET 3.5 5.4 - - - +
130B MET* 1.3 76.8 - - - +
132B GLN* 1.3 57.0 + - - +
134B ASN* 3.3 2.1 + - - -
135B LEU* 2.9 28.3 + - - +
428B ILE* 4.2 13.4 - - + +
431B PHE* 3.6 31.4 - - + -
435B TYR* 3.2 25.4 + - + -
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Residues in contact with GLN 132 (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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128B MET 3.0 16.7 + - - +
129B ALA* 3.7 8.9 + - - +
130B MET 3.3 0.2 - - - -
131B ALA* 1.3 75.4 - - - +
133B ALA* 1.3 71.6 + - - +
135B LEU* 3.3 0.6 + - - -
136B ALA* 3.0 25.8 + - - +
147B SER* 2.9 36.7 + - - +
148B ASP* 3.4 3.5 + - - -
149B ASN* 3.1 49.2 + - - +
151B THR* 5.2 0.9 - - - +
179B ASN* 3.9 19.4 - - + +
431B PHE* 3.9 16.1 - - + -
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 3.0 16.8 + - - +
130B MET* 3.3 6.0 + - - +
132B GLN* 1.3 86.3 - - - +
134B ASN* 1.3 57.9 + - - +
136B ALA* 3.9 3.5 - - - +
137B ALA* 3.0 29.3 + - - +
177B LEU* 4.8 4.7 - - + -
397B PHE* 4.0 3.6 - - + -
407B TYR* 3.6 39.8 - - + +
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Residues in contact with ASN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B MET 3.0 16.7 + - - +
131B ALA* 3.7 1.8 - - - +
132B GLN 3.2 0.2 - - - -
133B ALA* 1.3 73.9 - - - +
135B LEU* 1.3 57.8 + - - +
137B ALA* 3.3 0.9 + - - +
138B THR* 2.7 47.3 + - - +
333B ARG* 5.1 2.6 + - - -
374B PRO 5.5 1.0 - - - +
377B ILE* 4.1 13.8 - - + +
397B PHE* 4.1 6.0 - - + -
407B TYR 3.1 18.0 + - - +
408B SER 3.6 9.9 + - - -
409B GLY 3.1 25.9 + - - -
410B ARG* 4.3 2.8 - - - +
435B TYR* 2.6 34.6 + - + +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 4.2 17.9 - - + +
131B ALA 2.9 14.6 + - - +
132B GLN* 3.7 5.6 - - - +
134B ASN* 1.3 76.0 - - - +
136B ALA* 1.3 58.4 + - - +
138B THR* 4.5 0.2 - - - -
139B TYR* 2.8 62.2 + - + +
146B LEU* 5.7 2.5 - - + +
147B SER* 4.0 17.4 - - - +
330B LEU* 4.2 11.9 - - + -
333B ARG* 4.3 1.3 - - - +
431B PHE* 3.8 24.5 - - + -
433B ALA* 4.0 20.9 - - + -
435B TYR* 2.9 18.0 + - + +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN* 3.0 24.2 + - - +
133B ALA* 3.9 4.7 - - - +
135B LEU* 1.3 78.2 - - - +
137B ALA* 1.3 59.6 + - - +
140B ASN* 2.9 58.2 + - - +
147B SER* 3.4 17.9 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ALA 3.0 19.1 + - - +
134B ASN 3.3 0.4 + - - +
136B ALA* 1.3 77.1 - - - +
138B THR* 1.3 60.7 + - - +
140B ASN 5.2 2.1 - - - +
406B ASN* 6.0 0.4 - - - -
407B TYR* 3.5 10.8 - - + +
408B SER* 3.5 38.4 - - - +
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ASN* 2.7 41.7 + - - -
135B LEU 3.8 2.5 - - - -
137B ALA* 1.3 79.8 - - - +
139B TYR* 1.3 91.3 + - + +
140B ASN 3.9 0.7 - - - -
141B LYS* 5.0 4.5 + - - -
326B LEU* 4.6 14.8 - - + +
329B GLU* 4.8 4.0 - - - +
333B ARG* 5.1 2.7 - - - +
374B PRO* 6.1 2.9 - - + +
408B SER* 4.4 9.5 + - - -
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Residues in contact with TYR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 2.8 46.7 + - + +
138B THR* 1.3 91.5 - - + +
140B ASN* 1.3 67.8 + - - +
141B LYS* 3.6 3.7 - - - +
146B LEU* 4.4 15.0 - - + -
147B SER* 6.4 0.2 - - - -
319B TYR* 2.8 42.4 + - - +
326B LEU* 3.9 28.7 - - + -
329B GLU* 2.5 31.8 + - + +
330B LEU* 4.1 20.2 - - + -
333B ARG* 2.8 43.7 + - - -
374B PRO* 4.4 0.2 - - - +
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Residues in contact with ASN 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU 5.0 0.2 - - - +
136B ALA* 2.9 33.5 + - - +
137B ALA 5.2 2.1 - - - +
138B THR 5.1 1.0 - - - +
139B TYR* 1.3 79.6 + - - +
141B LYS* 1.3 71.8 + - - +
144B PHE 3.5 4.7 - - - +
145B THR* 4.0 12.4 - - - +
146B LEU* 2.8 31.4 + - - +
147B SER* 2.9 33.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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