Contacts of the helix formed by residues 129 - 146 (chain O) in PDB entry 5G04
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 THR 129 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLU* 3.4 38.6 - - + +
310I TRP* 5.4 0.2 - - - -
427I ARG* 4.0 36.0 - - - +
127O HIS* 3.0 17.4 + - - +
128O LYS* 1.3 85.1 + - - +
130O SER* 1.3 84.4 + - - +
133O GLY* 3.4 12.5 + - - -
134O LEU* 4.4 4.7 - - + -
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Residues in contact with SER 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307I LEU 5.2 0.3 + - - -
308I LEU 4.2 7.1 + - - -
309I LEU 3.1 24.9 - - - -
310I TRP* 3.5 0.8 - - - -
311I GLY* 3.0 27.8 + - - -
427I ARG* 4.2 12.4 + - - +
129O THR* 1.3 92.1 + - - +
131O VAL* 1.3 67.5 + - - +
132O VAL 4.2 0.7 - - - -
133O GLY 4.5 0.2 - - - -
134O LEU* 3.1 23.9 + - - +
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Residues in contact with VAL 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I LEU* 4.6 13.0 - - + +
309I LEU* 3.8 10.2 + - + +
442I GLN* 4.8 12.3 - - - +
445I ILE* 3.8 32.8 - - + -
65O LEU* 4.0 20.6 - - + -
68O LEU* 3.5 29.4 - - + -
69O GLN* 4.6 5.8 - - + +
130O SER* 1.3 74.3 - - - +
132O VAL* 1.3 59.5 + - + +
134O LEU* 4.1 2.6 - - - +
135O PHE* 3.0 33.6 + - + +
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Residues in contact with VAL 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309I LEU* 3.6 16.7 + - + +
310I TRP* 3.5 39.5 - - + +
41O LEU* 4.0 25.0 - - + +
64O LEU* 3.9 27.6 - - + -
68O LEU* 4.1 7.2 - - + -
126O VAL* 3.7 16.8 - - + -
130O SER 3.3 0.2 - - - -
131O VAL* 1.3 80.2 - - + +
133O GLY* 1.3 63.5 + - - +
135O PHE* 3.8 5.1 - - - +
136O LEU* 3.2 25.9 + - + +
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Residues in contact with GLY 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119O PHE* 3.7 0.9 - - - -
126O VAL* 3.9 17.2 - - - +
128O LYS* 4.1 9.4 - - - -
129O THR 3.4 20.2 + - - -
130O SER* 3.3 3.2 + - - -
131O VAL 3.2 0.6 - - - -
132O VAL* 1.3 79.0 - - - +
134O LEU* 1.3 56.9 + - - +
136O LEU* 3.4 5.2 + - - +
137O ARG* 3.0 36.9 + - - +
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Residues in contact with LEU 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D GLU* 4.4 16.6 - - + +
27D GLU* 3.7 52.5 - - + +
30D LEU* 3.8 5.0 - - + +
442I GLN* 5.9 2.0 - - - +
128O LYS 3.9 16.6 - - - +
129O THR* 4.4 3.8 - - + -
130O SER 3.1 21.4 + - - +
131O VAL* 4.2 2.2 - - - +
133O GLY* 1.3 72.5 - - - +
135O PHE* 1.3 66.4 + - - +
137O ARG* 3.3 16.5 + - - +
138O HIS* 2.9 38.8 + - + +
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Residues in contact with PHE 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O LYS* 3.9 41.1 - - + -
37O VAL* 4.4 11.9 - - + -
38O LEU* 4.0 21.8 - - + -
41O LEU* 4.0 27.1 - - + -
68O LEU* 4.0 35.9 - - + -
131O VAL* 3.0 21.4 + - + +
132O VAL* 3.8 4.9 - - - +
133O GLY 3.2 0.2 - - - -
134O LEU* 1.3 77.8 - - - +
136O LEU* 1.3 68.4 + - + +
138O HIS* 3.5 7.4 + - - +
139O MET* 3.2 36.1 + - + +
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Residues in contact with LEU 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O LEU* 4.2 17.5 - - + -
41O LEU* 5.8 3.4 - - + -
115O LEU* 4.1 21.8 - - + +
118O SER* 5.3 1.3 - - - +
119O PHE* 3.3 46.2 - - + -
126O VAL* 3.7 22.7 - - + -
132O VAL* 3.2 12.4 + - + +
133O GLY 3.7 3.1 - - - +
135O PHE* 1.3 84.9 - - + +
137O ARG* 1.3 53.0 + - - +
139O MET* 3.1 6.8 + - - +
140O ILE* 2.7 63.5 + - + +
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Residues in contact with ARG 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLU* 4.9 4.9 + - - +
30D LEU* 3.5 38.3 - - + +
31D GLN* 4.7 17.0 - - - +
34D GLU* 2.8 32.2 + - - +
119O PHE* 3.6 20.2 - - + -
128O LYS* 3.4 48.9 + - - +
133O GLY 3.0 22.3 + - - +
134O LEU* 3.3 13.7 + - - +
136O LEU* 1.3 78.7 - - + +
138O HIS* 1.3 55.7 + - - +
140O ILE* 3.2 8.1 + - + +
141O LEU* 2.8 32.4 + - - +
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Residues in contact with HIS 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLU* 3.1 45.3 + - + +
30D LEU* 3.5 31.1 + - + +
33D GLN* 5.1 8.0 + - - -
28O ASP* 4.0 33.7 + - + +
134O LEU* 2.9 32.5 + - + +
135O PHE* 3.8 7.1 - - + +
137O ARG* 1.3 73.2 - - - +
139O MET* 1.3 63.6 + - + +
141O LEU* 3.9 6.3 - - + +
142O ALA* 2.9 30.9 + - - +
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Residues in contact with MET 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28O ASP* 3.9 22.9 - - - +
29O TRP 4.7 4.5 - - - +
30O VAL* 3.7 30.7 - - + +
34O LYS* 3.6 44.0 - - + -
38O LEU* 3.8 23.8 - - + -
112O PHE* 4.0 2.6 - - + -
135O PHE* 3.2 36.5 + - + +
136O LEU 3.1 8.3 + - - +
138O HIS* 1.3 80.1 - - + +
140O ILE* 1.3 65.2 + - - +
142O ALA* 5.4 0.7 - - - -
143O TYR* 2.9 26.5 + - - +
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Residues in contact with ILE 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O PHE* 4.7 11.7 - - + +
115O LEU* 4.1 16.6 - - + +
116O SER* 3.6 42.2 - - - +
119O PHE* 5.4 4.9 - - + -
136O LEU* 2.7 46.4 + - + +
137O ARG* 3.5 7.9 - - + +
139O MET* 1.3 71.4 - - - +
141O LEU* 1.3 66.9 + - + +
143O TYR* 3.4 3.5 + - - +
144O SER* 3.0 29.2 + - - +
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Residues in contact with LEU 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 4.8 13.5 - - + +
33D GLN* 3.8 43.5 - - + +
34D GLU* 4.4 11.2 - - + +
37D HIS* 3.6 40.8 - - + -
137O ARG 2.8 17.3 + - - +
138O HIS* 3.9 7.4 - - + +
140O ILE* 1.3 79.4 - - + +
142O ALA* 1.3 58.7 + - - +
144O SER* 3.2 7.5 + - - -
145O LYS* 3.0 38.3 + - - +
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Residues in contact with ALA 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O ASP* 4.2 10.5 - - + +
29O TRP* 3.9 28.7 - - + -
30O VAL* 4.0 8.5 - - + -
138O HIS 2.9 20.1 + - - +
139O MET* 3.8 3.6 - - - +
141O LEU* 1.3 75.7 - - - +
143O TYR* 1.3 64.1 + - - +
145O LYS* 3.7 7.7 + - - +
146O LEU* 3.1 29.5 + - - +
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Residues in contact with TYR 143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O VAL* 3.9 6.4 - - + +
108O MET* 4.6 1.6 - - - -
109O GLU* 3.0 46.8 + - + +
112O PHE* 3.5 58.8 - + + -
113O ASP* 4.5 7.6 - - - -
139O MET 2.9 17.3 + - - +
140O ILE 4.0 1.8 - - - +
142O ALA* 1.3 78.3 - - - +
144O SER* 1.3 76.5 + - - +
146O LEU* 3.2 22.0 + - - +
151O VAL* 3.5 37.2 - - + +
154O LEU* 4.3 5.4 - - + -
341P TYR* 5.3 1.3 + - - -
346P GLN* 4.5 15.3 + - - -
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Residues in contact with SER 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D HIS* 3.5 29.1 + - - -
40D TRP* 5.2 3.3 - - - -
140O ILE* 3.0 24.5 + - - +
141O LEU* 3.6 5.2 - - - -
143O TYR* 1.3 88.1 - - - +
145O LYS* 1.3 60.3 + - - +
146O LEU 3.5 5.2 + - - +
346P GLN* 5.3 8.2 + - - +
349P LYS* 4.5 15.9 + - - +
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Residues in contact with LYS 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D GLN* 4.8 19.3 + - - +
36D GLN* 5.6 1.0 - - - +
37D HIS* 3.3 40.3 - - + +
40D TRP* 5.9 4.5 - - - -
141O LEU* 3.0 29.1 + - - +
142O ALA* 3.9 9.0 - - - +
143O TYR 3.3 0.4 - - - -
144O SER* 1.3 78.1 - - - +
146O LEU* 1.3 63.3 + - + +
147O SER* 3.6 1.2 + - - -
150O GLN* 4.6 1.5 - - - +
349P LYS* 4.9 4.0 + - - -
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Residues in contact with LEU 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 4.9 5.4 - - + -
29O TRP* 4.4 26.9 - - + -
30O VAL* 5.0 6.7 - - + +
142O ALA 3.1 22.7 - - - +
143O TYR* 3.2 9.9 + - - +
144O SER 4.0 5.7 - - - +
145O LYS* 1.3 80.7 - - + +
147O SER* 1.3 66.1 + - - +
148O PHE 3.8 0.2 + - - -
150O GLN* 3.2 31.0 - - + +
151O VAL* 3.2 43.6 - - + +
154O LEU* 4.3 17.5 - - + -
341P TYR* 4.5 3.5 + - - -
349P LYS* 4.0 8.4 + - - +
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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