Contacts of the helix formed by residues 113 - 129 (chain F) 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 SER 113 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69F PRO* 4.6 6.9 - - - +
70F GLN* 5.5 6.0 + - - +
73F TYR* 5.9 2.0 - - - +
110F PHE* 2.9 26.9 + - - +
112F ASP* 1.3 78.7 + - - +
114F ALA* 1.3 62.7 + - - +
115F CYS 3.2 2.2 + - - -
116F PHE* 3.3 19.2 + - - +
117F THR* 3.4 16.6 + - - +
18H HIS* 3.1 33.4 - - - -
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Residues in contact with ALA 114 (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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106F ILE 4.0 2.0 - - - +
107F VAL* 3.7 36.8 - - + +
110F PHE* 3.7 10.9 + - + -
111F GLY 3.0 21.0 + - - +
112F ASP 3.1 0.4 - - - -
113F SER* 1.3 74.8 + - - +
115F CYS* 1.3 65.8 + - - +
117F THR* 2.6 25.0 + - - +
118F LEU* 3.0 14.5 + - + +
144F LEU* 4.4 6.3 - - + -
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Residues in contact with CYS 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F ASP 3.9 12.1 + - - +
113F SER 3.2 1.0 - - - -
114F ALA* 1.3 78.2 - - - +
116F PHE* 1.3 104.0 + - - +
118F LEU* 3.3 0.3 + - - +
119F SER* 3.0 19.1 + - - -
141F SER* 3.6 18.9 - - - +
144F LEU* 3.8 26.6 - - + +
145F ASN* 3.5 32.1 - - - +
148F LEU* 4.1 14.6 - - + -
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Residues in contact with PHE 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F TYR* 4.1 8.8 + - + +
112F ASP* 5.3 0.9 - - - -
113F SER* 3.3 11.0 + - - +
114F ALA 3.3 0.2 - - - -
115F CYS* 1.3 102.9 - - - +
117F THR* 1.4 51.8 - - - +
119F SER* 3.1 11.0 + - - -
120F LEU* 2.9 32.4 + - - +
145F ASN* 6.0 1.3 - - - -
148F LEU* 3.7 29.2 - - + -
11H ALA 4.6 1.1 - - - -
14H GLN* 3.6 45.5 - - + -
15H ALA* 3.6 24.5 - - + -
18H HIS* 3.5 41.5 - + + -
20H ALA* 4.5 13.2 - - + -
23H ASP* 4.8 0.4 - - - -
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Residues in contact with THR 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F TYR* 3.4 34.3 - - + -
92F LEU* 4.1 16.3 - - + +
106F ILE* 3.9 14.9 - - - +
110F PHE* 3.7 31.1 - - + -
113F SER* 3.4 15.3 - - - +
114F ALA* 2.6 24.9 + - - -
116F PHE* 1.4 72.1 - - + +
118F LEU* 1.3 53.4 + - - +
120F LEU* 3.3 2.5 + - - +
121F LEU* 2.8 35.2 + - - +
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Residues in contact with LEU 118 (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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103F HIS* 3.5 30.1 - - + +
106F ILE* 3.8 28.9 - - + -
107F VAL* 3.9 24.7 - - + -
114F ALA* 3.0 19.5 + - + +
115F CYS 3.6 4.3 - - - +
117F THR* 1.3 73.6 + - - +
119F SER* 1.3 60.3 + - - +
121F LEU* 4.0 3.8 - - + -
122F GLY* 2.8 23.9 + - - -
137F CYS* 2.9 24.7 - - - +
140F LYS* 3.7 29.6 - - + -
141F SER* 4.3 5.6 - - - +
144F LEU* 3.9 11.7 - - + -
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Residues in contact with SER 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F CYS 3.0 12.5 + - - -
116F PHE* 3.1 12.8 + - - -
118F LEU* 1.3 74.7 - - - +
120F LEU* 1.3 65.5 + - - +
122F GLY* 3.1 2.8 + - - -
123F HIS* 3.0 20.7 + - - +
138F TYR* 3.5 15.2 - - - -
141F SER* 4.1 15.0 + - - -
148F LEU* 5.2 4.7 - - - -
150F SER* 4.1 16.1 + - - -
151F PRO* 4.2 14.4 - - - +
23H ASP* 5.1 0.7 + - - -
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Residues in contact with LEU 120 (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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73F TYR* 3.5 29.4 - - + +
76F ALA* 4.1 1.1 - - + -
77F LYS* 4.0 34.5 - - + +
80F VAL* 3.9 33.4 - - + -
92F LEU* 3.9 22.4 - - + -
116F PHE 2.9 11.3 + - - +
117F THR* 3.5 7.0 - - - +
119F SER* 1.3 73.1 - - - +
121F LEU* 1.3 67.3 + - - +
123F HIS* 3.1 12.4 + - + +
124F VAL* 3.0 26.6 + - + +
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Residues in contact with LEU 121 (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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89F GLU* 4.3 15.3 - - + +
92F LEU* 4.4 20.0 - - + -
93F SER* 4.4 9.4 - - - +
103F HIS* 4.4 2.0 - - + -
106F ILE* 4.1 28.0 - - + -
117F THR 2.8 19.1 + - - +
118F LEU* 3.5 9.4 - - + +
120F LEU* 1.3 77.5 - - - +
122F GLY* 1.3 60.4 + - - +
124F VAL* 3.3 11.1 + - + +
125F TYR* 3.1 56.0 + - + +
137F CYS* 3.7 16.2 - - - -
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Residues in contact with GLY 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F LEU 2.8 16.1 + - - -
119F SER 3.1 5.3 + - - -
121F LEU* 1.3 73.2 - - - +
123F HIS* 1.3 62.7 + - - +
125F TYR* 3.0 5.8 + - - +
126F CYS* 2.9 27.5 + - - -
134F GLY 4.3 2.2 - - - -
137F CYS* 3.6 16.6 - - - -
138F TYR* 3.5 18.8 - - - -
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Residues in contact with HIS 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F VAL* 4.4 22.4 - - + +
119F SER 3.0 11.3 + - - +
120F LEU* 3.3 15.9 - - + +
122F GLY* 1.3 74.0 - - - +
124F VAL* 1.3 63.4 + - - +
126F CYS* 3.5 1.5 + - - +
127F LYS* 3.2 36.3 + - + +
138F TYR* 3.1 19.3 + - + +
154F SER* 5.3 4.2 + - - -
599F ASN* 5.5 6.3 + - - -
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Residues in contact with VAL 124 (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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80F VAL* 3.8 28.0 - - + -
85F LEU* 3.8 32.5 - - + +
88F GLY 5.5 0.9 - - - -
89F GLU* 4.0 22.4 - - + +
92F LEU* 5.5 2.9 - - + -
120F LEU* 3.0 20.5 + - + +
121F LEU* 3.5 14.4 - - + +
122F GLY 3.2 0.2 - - - -
123F HIS* 1.3 73.5 - - - +
125F TYR* 1.3 53.6 + - - +
127F LYS* 3.4 5.8 + - - +
128F THR* 2.3 50.1 + - - +
130F ARG* 4.8 0.7 - - - +
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Residues in contact with TYR 125 (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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89F GLU* 3.1 17.9 + - - -
93F SER* 3.9 11.6 - - - -
103F HIS* 4.4 10.8 - + - -
106F ILE* 6.0 0.2 - - - +
121F LEU* 3.1 51.1 + - + +
122F GLY 3.0 5.9 + - - +
124F VAL* 1.3 76.3 - - - +
126F CYS* 1.3 63.0 + - - +
128F THR* 3.1 4.6 + - - -
129F ASP 3.0 4.5 + - - -
130F ARG* 2.7 80.8 + - + +
133F LYS* 4.1 25.3 + - + -
134F GLY* 3.6 22.9 - - - -
137F CYS* 4.0 14.8 - - + -
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Residues in contact with CYS 126 (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 GLY 2.9 12.5 + - - +
123F HIS* 4.1 3.4 - - - +
125F TYR* 1.3 77.6 - - - +
127F LYS* 1.3 61.8 + - - +
129F ASP* 3.1 13.0 + - - -
131F LEU* 4.0 28.4 - - + +
134F GLY* 4.1 15.5 - - - -
138F TYR* 3.4 23.6 - - - +
158F ILE* 3.3 33.2 - - + -
632F PRO* 5.9 2.8 - - - +
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Residues in contact with LYS 127 (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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80F VAL* 5.7 5.2 + - + +
83F SER* 4.6 20.0 + - - +
85F LEU* 3.6 35.4 - - + +
123F HIS* 3.2 28.7 + - + +
124F VAL* 3.7 5.4 - - - +
126F CYS* 1.3 76.5 - - - +
128F THR* 1.3 61.8 + - - +
129F ASP* 3.2 2.3 + - - +
599F ASN* 3.7 36.3 + - - +
629F ARG 5.7 1.9 - - - +
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Residues in contact with THR 128 (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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85F LEU* 3.9 23.4 - - + +
89F GLU* 5.3 0.7 - - - +
124F VAL* 2.3 42.4 + - - +
125F TYR 3.1 7.2 + - - -
127F LYS* 1.3 72.2 - - - +
129F ASP* 1.3 66.1 + - - +
130F ARG* 3.4 35.8 + - - +
506Y GLN* 3.7 10.0 - - + +
508Y ASP* 3.7 20.8 - - - +
512Y HIS* 5.3 0.2 + - - -
534Y ILE* 5.6 1.0 - - - +
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Residues in contact with ASP 129 (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 TYR 3.0 2.4 + - - -
126F CYS 3.1 12.8 + - - -
127F LYS 3.1 3.1 + - - +
128F THR* 1.3 79.3 - - - +
130F ARG* 1.3 55.9 + - - +
131F LEU* 2.9 19.7 + - - +
503Y LEU* 5.1 1.9 - - - +
506Y GLN* 3.0 27.4 + - + +
512Y HIS* 3.5 19.3 - - + -
531Y GLN* 5.3 3.5 - - - +
534Y ILE* 4.7 22.6 - - + +
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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
------------------------------------------------------------
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