Contacts of the helix formed by residues 120 - 140 (chain B) in PDB entry 1GO4
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 SER 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LYS* 1.3 75.1 - - - +
121B GLN* 1.3 65.4 + - - +
122B LYS* 4.0 6.4 - - - +
123B ALA* 2.9 44.4 + - - +
124B ILE* 3.2 17.4 + - - +
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLY 4.5 11.9 + - - +
11B ILE* 3.7 21.6 - - - +
19B ILE* 3.4 26.7 - - - +
119B LYS 3.7 1.2 + - - +
120B SER* 1.3 73.3 - - - +
122B LYS* 1.3 57.5 + - - +
124B ILE* 3.6 5.3 + - - +
125B GLN* 3.0 40.6 + - + +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TYR 6.2 0.8 - - - -
50B GLY* 5.9 4.9 - - - +
120B SER* 3.1 6.3 - - - +
121B GLN* 1.3 78.7 - - - +
123B ALA* 1.3 61.6 + - - +
125B GLN* 3.8 19.6 + - + +
126B ASP* 2.4 55.9 + - - +
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Residues in contact with ALA 123 (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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119B LYS* 3.4 25.6 - - + -
120B SER* 2.9 25.7 + - - +
122B LYS* 1.3 77.4 - - - +
124B ILE* 1.3 60.8 + - - +
126B ASP* 3.2 10.4 + - - +
127B GLU* 3.1 26.0 + - - +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.6 31.4 - - + -
19B ILE* 4.2 24.0 - - + -
119B LYS* 3.3 28.3 - - + +
120B SER 3.2 6.0 + - - +
121B GLN* 3.9 7.0 - - - +
123B ALA* 1.3 72.4 - - - +
125B GLN* 1.3 61.8 + - + +
127B GLU* 3.1 6.3 + - - +
128B ILE* 2.9 31.3 + - + +
186B PHE* 4.2 14.6 - - + -
187B THR 4.0 4.3 - - - +
188B THR* 3.8 38.8 - - + -
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LYS* 4.8 14.6 - - - +
49B TYR* 4.0 40.2 - - + +
121B GLN* 3.0 33.2 + - + +
122B LYS* 3.8 26.0 - - + +
124B ILE* 1.3 77.0 - - + +
126B ASP* 1.3 57.5 + - - +
128B ILE* 3.7 5.5 - - + +
129B ARG* 2.9 28.1 + - - +
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Residues in contact with ASP 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LYS* 2.4 56.6 + - - +
123B ALA* 3.4 9.0 - - - +
124B ILE 3.1 0.2 - - - -
125B GLN* 1.3 75.8 - - - +
127B GLU* 1.3 66.1 + - + +
129B ARG* 3.4 15.1 + - - +
130B SER* 3.2 23.0 + - - -
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LYS* 3.1 26.2 + - - -
123B ALA* 3.1 16.1 + - - +
124B ILE* 3.1 6.2 + - - +
126B ASP* 1.3 76.6 - - + +
128B ILE* 1.3 62.8 + - - +
130B SER* 3.2 9.7 + - - -
131B VAL* 3.1 24.3 + - - +
185B SER 4.4 4.6 - - - +
186B PHE* 3.4 16.1 - - + +
187B THR* 2.9 38.7 + - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.1 19.7 - - + -
23B PHE* 3.7 20.2 - - + -
49B TYR* 3.6 51.8 - - + +
124B ILE* 2.9 23.0 + - + +
125B GLN* 3.7 6.3 - - + +
127B GLU* 1.3 74.5 - - - +
129B ARG* 1.3 67.4 + - - +
131B VAL* 2.9 18.6 + - - +
132B ILE* 3.0 14.6 + - + +
186B PHE* 3.8 38.1 - - + -
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Residues in contact with ARG 129 (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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49B TYR* 3.0 33.2 - - - +
50B GLY* 3.8 17.3 + - - -
51B LEU* 3.7 26.8 - - + +
125B GLN 2.9 17.1 + - - +
126B ASP* 3.5 16.1 + - - +
127B GLU 3.3 0.2 - - - -
128B ILE* 1.3 77.1 - - - +
130B SER* 1.3 65.8 + - - +
132B ILE* 3.4 1.2 + - - -
133B ALA* 2.9 33.1 + - + +
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Residues in contact with SER 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP 3.2 10.7 + - - -
127B GLU* 3.5 10.8 - - - -
128B ILE 3.1 0.4 - - - -
129B ARG* 1.3 87.1 + - - +
131B VAL* 1.3 64.5 + - - +
133B ALA* 4.3 5.2 - - - +
134B GLN* 3.1 25.1 + - - +
184B ARG* 3.9 35.7 + - - +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 4.0 27.4 - - + -
127B GLU 3.1 9.7 + - - +
128B ILE* 2.9 11.6 + - - +
130B SER* 1.3 76.0 - - - +
132B ILE* 1.3 64.4 + - - +
134B GLN* 3.4 3.1 + - - +
135B ILE* 3.2 27.8 + - + +
184B ARG* 3.6 18.6 - - + +
185B SER* 3.5 36.3 - - - +
186B PHE* 4.1 9.2 - - + +
193B VAL* 6.1 1.3 - - + -
195B SER* 4.0 23.4 + - - +
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 4.0 20.4 - - + -
26B PHE* 4.6 7.4 - - + -
27B GLY* 4.7 8.5 - - - +
30B SER* 4.3 15.0 - - - +
49B TYR* 3.8 34.3 - - + -
51B LEU* 4.0 8.5 - - + -
53B LEU* 3.8 33.9 - - + -
128B ILE* 3.0 17.2 + - + +
129B ARG 3.9 2.9 - - - +
131B VAL* 1.3 74.2 - - + +
133B ALA* 1.3 65.1 + - - +
135B ILE* 3.2 13.8 + - + +
136B THR* 3.1 24.4 + - - +
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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
----------------------------------------------------------
51B LEU* 4.3 18.3 - - + +
129B ARG* 2.9 25.6 + - + +
130B SER* 4.3 4.3 - - - +
132B ILE* 1.3 74.3 - - - +
134B GLN* 1.3 61.4 + - - +
136B THR* 3.2 10.4 + - - -
137B ALA* 2.8 29.5 + - - +
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Residues in contact with GLN 134 (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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130B SER 3.1 18.3 + - - +
131B VAL 3.6 4.9 - - - +
132B ILE 3.2 0.2 - - - -
133B ALA* 1.3 74.3 - - - +
135B ILE* 1.3 61.8 + - - +
137B ALA* 3.1 8.3 + - - +
138B THR* 2.8 35.9 + - - -
183B LEU* 4.3 25.8 - - + +
184B ARG* 3.8 33.9 + - + +
495G ARG* 3.8 36.2 - - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 5.7 1.6 - - + -
27B GLY* 5.3 5.2 - - - +
30B SER* 5.5 5.6 - - - +
31B ILE* 4.2 22.2 - - + -
34B GLN* 4.2 11.4 - - - +
100B TRP* 3.7 28.5 - - + -
102B PHE* 4.1 30.3 - - + -
131B VAL* 3.2 20.6 + - + +
132B ILE* 3.2 16.5 + - + +
133B ALA 3.2 0.2 - - - -
134B GLN* 1.3 76.8 - - - +
136B THR* 1.3 64.6 + - - +
138B THR* 2.9 17.9 + - - -
139B VAL* 3.1 16.6 + - + +
183B LEU* 4.3 12.3 - - + -
195B SER* 5.1 3.6 - - - +
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Residues in contact with THR 136 (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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30B SER* 5.9 0.2 - - - -
34B GLN* 3.1 38.8 + - - +
53B LEU* 6.1 0.2 - - - +
132B ILE* 3.1 17.7 + - - +
133B ALA* 3.2 12.6 + - - -
135B ILE* 1.3 77.3 - - - +
137B ALA* 1.3 61.3 + - - +
138B THR 3.2 0.9 + - - -
139B VAL* 3.4 15.0 + - - +
140B THR* 4.0 7.4 + - - -
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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
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133B ALA 2.8 20.3 + - - +
134B GLN* 3.1 14.5 + - - +
136B THR* 1.3 73.8 - - - +
138B THR* 1.3 60.4 + - - +
140B THR* 3.9 8.1 - - - -
141B PHE* 3.4 13.9 - - - -
495G ARG* 2.8 30.4 + - - +
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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
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100B TRP* 4.5 4.3 - - + -
134B GLN* 2.8 18.6 + - - -
135B ILE* 2.9 12.3 + - - -
137B ALA* 1.3 76.2 - - - +
139B VAL* 1.3 65.3 + - - +
140B THR 3.1 2.2 - - - -
141B PHE* 2.9 17.3 + - - +
142B LEU* 3.6 29.2 + - + +
181B VAL* 5.3 0.4 - - + -
183B LEU* 3.3 25.9 - - + +
197B VAL* 4.4 16.2 - - + -
492G LEU* 4.0 18.8 - - + +
495G ARG* 4.0 7.7 + - - +
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 6.4 0.2 - - - -
34B GLN* 3.5 40.8 - - + +
35B ARG* 3.9 31.1 + - + +
100B TRP* 4.4 11.9 - - + -
135B ILE* 3.1 16.7 + - + +
136B THR 3.4 8.7 + - - +
138B THR* 1.3 76.1 - - - +
140B THR* 1.3 64.2 + - - +
142B LEU* 3.1 25.4 + - - +
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Residues in contact with THR 140 (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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136B THR 4.0 8.6 + - - -
137B ALA* 3.9 14.2 + - - -
139B VAL* 1.3 79.0 - - - +
141B PHE* 1.3 83.4 + - + +
142B LEU 3.8 2.9 + - - +
488G GLU* 5.5 1.2 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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