Contacts of the helix formed by residues 119 - 141 (chain F) in PDB entry 4GTU
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 PHE 119 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F VAL* 3.7 18.8 - - + -
114F CYS* 5.1 0.9 - - - -
116F SER 2.8 16.6 + - - +
117F PRO 4.0 5.2 - - - +
118F ASP* 1.3 74.0 - - - +
120F GLU* 1.3 84.3 + - + +
121F LYS 2.7 12.7 + - - -
122F LEU* 3.0 11.5 + - - +
123F LYS* 2.8 68.0 + - + +
169F PHE* 4.0 13.2 - + - -
213F VAL* 3.6 24.0 - - + -
214F TRP* 4.0 34.1 - + + -
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Residues in contact with GLU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ASP 2.5 8.5 + - - +
119F PHE* 1.3 102.4 - - + +
121F LYS* 1.3 59.8 + - + +
123F LYS* 3.9 16.2 + - - +
124F PRO* 3.0 23.4 - - - +
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Residues in contact with LYS 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ASP* 3.0 25.1 + - + +
119F PHE 2.7 5.9 + - - -
120F GLU* 1.3 78.0 - - + +
122F LEU* 1.3 58.5 + - + +
124F PRO* 3.4 16.1 - - - +
125F GLU* 3.2 14.5 - - - +
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Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F VAL* 4.5 19.9 - - + +
116F SER* 3.6 29.8 - - - +
118F ASP* 4.0 10.3 - - + +
119F PHE* 3.0 36.7 + - - +
121F LYS* 1.3 76.3 - - + +
123F LYS* 1.3 65.0 + - - +
124F PRO 3.5 0.2 - - - -
125F GLU* 3.0 32.8 - - + +
126F TYR* 3.0 12.7 + - - +
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Residues in contact with LYS 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F VAL* 4.1 10.5 - - + -
119F PHE* 2.8 65.9 + - + +
120F GLU* 3.9 14.4 + - - +
122F LEU* 1.3 77.0 - - - +
124F PRO* 1.4 71.6 - - + +
126F TYR* 3.0 19.7 + - + +
127F LEU* 3.1 25.7 + - + +
169F PHE* 3.7 28.0 - - + -
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Residues in contact with PRO 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F GLU* 3.0 27.1 - - - +
121F LYS 3.4 13.2 - - - +
123F LYS* 1.4 97.8 - - + +
125F GLU* 1.3 62.5 + - + +
127F LEU* 3.2 22.1 + - + +
128F GLU* 3.4 14.7 + - - +
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F LYS* 3.2 17.9 - - - +
122F LEU* 3.0 37.0 - - + +
124F PRO* 1.3 77.2 - - + +
126F TYR* 1.3 65.0 + - - +
128F GLU* 3.0 39.2 + - - +
129F GLU* 3.0 16.2 - - - +
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Residues in contact with TYR 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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106F VAL* 3.9 10.2 + - - +
109F GLN* 4.8 14.2 + - + +
110F LEU* 3.3 42.6 + - + +
113F VAL* 4.4 19.3 - - + -
122F LEU 3.0 14.1 + - - +
123F LYS* 3.1 15.5 - - - +
125F GLU* 1.3 78.2 - - - +
127F LEU* 1.3 58.2 + - + +
128F GLU 3.0 1.7 + - - -
129F GLU* 3.2 10.5 + - - +
130F LEU* 3.0 48.7 + - + +
133F MET* 3.6 27.3 - - + +
166F HIS* 2.9 26.1 + + - -
169F PHE* 5.2 5.8 - + - -
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Residues in contact with LEU 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F LYS* 3.1 32.2 + - + +
124F PRO* 3.2 13.0 + - + +
126F TYR* 1.3 80.5 - - + +
128F GLU* 1.3 57.1 + - - +
130F LEU* 4.0 25.3 - - + +
131F PRO* 3.0 24.9 - - - +
169F PHE* 4.6 12.8 - - + -
170F GLU* 4.1 35.9 - - + +
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Residues in contact with GLU 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F PRO 3.5 9.9 - - - +
125F GLU* 3.0 34.7 + - - +
126F TYR 2.9 1.0 - - - -
127F LEU* 1.3 80.9 - - - +
129F GLU* 1.3 67.3 + - + +
131F PRO* 3.4 8.7 - - - +
132F THR* 4.5 7.3 - - - +
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Residues in contact with GLU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F GLU* 3.0 25.6 - - - +
126F TYR* 3.2 13.2 + - - +
128F GLU* 1.3 81.7 - - + +
130F LEU* 1.3 65.8 + - - +
131F PRO 3.3 1.6 - - - -
132F THR* 3.2 14.2 + - + +
133F MET* 3.0 41.8 + - + +
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Residues in contact with LEU 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F TYR* 3.0 34.4 + - + +
127F LEU* 4.0 24.7 - - + -
129F GLU* 1.3 76.4 - - - +
131F PRO* 1.3 74.4 - - + +
133F MET* 3.1 19.5 + - + +
134F MET* 3.0 26.5 + - + +
166F HIS* 3.5 33.0 - - + -
169F PHE* 5.6 2.9 - - + -
170F GLU* 5.3 3.8 - - + -
173F CYS* 3.3 38.1 - - + -
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Residues in contact with PRO 131 (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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127F LEU 3.0 25.1 - - - +
128F GLU 3.4 10.5 - - - +
130F LEU* 1.3 97.1 - - + +
132F THR* 1.3 51.9 + - + +
134F MET* 2.9 9.8 + - + +
135F GLN* 2.7 33.4 + - - +
173F CYS* 5.5 6.3 - - + -
177F PHE* 3.7 16.5 - - + -
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Residues in contact with THR 132 (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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128F GLU 4.5 10.1 - - - +
129F GLU* 3.2 15.7 + - - +
131F PRO* 1.3 75.7 - - + +
133F MET* 1.3 65.5 + - - +
135F GLN* 3.1 33.5 + - - +
136F HIS* 2.8 33.1 + - - -
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Residues in contact with MET 133 (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 VAL* 5.4 12.6 - - + -
109F GLN* 4.0 20.0 - - - +
126F TYR* 3.6 29.8 - - + +
129F GLU* 3.0 37.3 + - + +
130F LEU* 3.2 32.8 - - - +
132F THR* 1.3 81.7 + - - +
134F MET* 1.3 62.4 + - + +
136F HIS* 3.3 18.1 + - + +
137F PHE* 3.2 25.2 - - + -
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Residues in contact with MET 134 (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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130F LEU* 3.0 17.4 + - + +
131F PRO* 2.9 9.9 + - + +
133F MET* 1.3 74.9 - - + +
135F GLN* 1.3 64.4 + - - +
136F HIS 3.1 1.8 - - - -
137F PHE* 3.0 13.0 + - + +
138F SER* 2.9 20.6 + - - -
163F LEU* 5.2 4.0 - - + -
166F HIS* 5.1 7.6 - - + +
173F CYS* 3.3 50.3 - - - +
174F LEU* 3.4 42.2 - - + -
177F PHE* 3.7 14.6 - - + -
180F LEU* 3.6 17.5 - - + +
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Residues in contact with GLN 135 (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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131F PRO 2.7 15.9 + - - +
132F THR* 3.1 29.6 - - - +
134F MET* 1.3 72.1 - - - +
136F HIS* 1.3 71.0 + - + +
138F SER* 3.2 6.2 + - - -
139F GLN* 3.2 32.3 + - + +
177F PHE* 3.7 26.1 - - + -
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Residues in contact with HIS 136 (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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49E LYS* 6.0 2.7 - - - -
50E PHE* 5.6 8.6 - + - -
55E ASP 4.1 20.4 - - - +
56E PHE* 4.2 16.5 - - + -
57E PRO* 4.3 28.2 - - + +
132F THR* 2.8 35.9 + - - -
133F MET* 3.5 14.3 + - + +
134F MET 3.1 0.2 - - - -
135F GLN* 1.3 89.1 + - + +
137F PHE* 1.3 64.2 + - - +
139F GLN* 3.7 14.8 + - - +
140F PHE* 3.2 22.2 + - - +
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Residues in contact with PHE 137 (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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56E PHE* 3.6 24.2 - + - -
99F LEU* 3.9 20.9 - - + -
102F GLN* 4.2 11.9 - - + -
103F ALA* 4.9 7.6 - - + -
106F VAL* 3.6 36.3 - - + -
133F MET* 3.2 27.4 - - + -
134F MET* 3.0 13.5 + - + +
136F HIS* 1.3 75.0 - - - +
138F SER* 1.3 68.0 + - - +
140F PHE* 3.2 7.2 + - - +
141F LEU* 3.1 23.6 + - - +
147F PHE* 3.8 25.0 - + + -
159F ALA* 6.1 4.5 - - + -
162F VAL* 5.5 6.5 - - + -
163F LEU* 5.3 9.6 - - + -
180F LEU* 4.0 13.2 - - + -
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Residues in contact with SER 138 (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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134F MET 2.9 12.1 + - - -
135F GLN 3.4 9.0 - - - -
137F PHE* 1.3 78.6 - - - +
139F GLN* 1.3 57.9 + - - +
142F GLY* 2.8 15.1 + - - -
177F PHE* 3.8 26.6 - - - +
179F ASN* 2.5 50.1 + - - +
180F LEU* 3.6 12.0 - - - +
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Residues in contact with GLN 139 (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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135F GLN* 3.2 19.7 + - + +
136F HIS* 3.9 19.4 - - - +
138F SER* 1.3 80.2 - - - +
140F PHE* 1.3 63.6 + - - +
141F LEU 3.2 1.0 + - - -
142F GLY* 3.2 13.9 + - - +
144F ARG* 4.3 2.4 + - - -
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Residues in contact with PHE 140 (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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55E ASP* 3.4 44.9 - - + -
56E PHE* 3.9 15.7 - + + -
95F ARG* 3.4 60.3 + - + +
98F ILE* 4.3 9.2 - - + -
99F LEU* 4.0 29.6 - - + -
136F HIS 3.2 12.2 + - - +
137F PHE 3.2 9.8 + - - +
139F GLN* 1.3 77.1 - - - +
141F LEU* 1.3 52.1 + - - +
144F ARG* 2.4 28.9 + - - -
147F PHE* 3.5 27.7 - + + +
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Residues in contact with LEU 141 (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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137F PHE 3.1 11.1 + - - +
138F SER 3.6 6.3 - - - +
140F PHE* 1.3 77.8 - - - +
142F GLY* 1.3 65.5 + - - +
143F LYS 2.9 2.9 + - - -
144F ARG* 2.8 55.3 + - - +
145F PRO 3.4 14.4 - - - +
147F PHE* 3.7 32.1 - - + +
179F ASN* 3.4 23.3 - - - +
180F LEU* 3.5 22.7 - - + -
183F PHE* 3.6 29.2 - - + -
186F ARG* 4.8 2.7 - - - +
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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