Contacts of the helix formed by residues 130 - 145 (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 ARG 130 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F GLU* 2.9 40.5 + - - +
96F VAL* 6.0 0.6 - - - +
124F VAL* 4.8 0.2 - - - +
125F TYR* 2.7 50.5 + - + +
128F THR* 3.3 28.3 + - - +
129F ASP* 1.3 73.9 - - - +
131F LEU* 1.3 60.3 + - - +
132F ALA 3.4 2.2 - - - -
133F LYS* 3.4 23.0 + - + +
134F GLY 3.0 16.6 + - - -
504Y ALA 3.0 20.4 - - - +
505Y ASN 2.6 31.0 + - - -
506Y GLN* 2.9 50.6 + - + +
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Residues in contact with LEU 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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126F CYS* 4.0 27.9 - - + +
129F ASP* 2.9 17.4 + - - +
130F ARG* 1.3 69.9 - - - +
132F ALA* 1.3 64.4 + - - +
134F GLY* 3.1 1.0 + - - -
135F SER* 3.0 29.4 + - - -
158F ILE* 3.5 45.5 - - + -
159F GLY* 5.0 4.0 - - - +
632F PRO* 5.0 21.5 - - + -
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Residues in contact with ALA 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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130F ARG 3.4 0.4 - - - -
131F LEU* 1.3 79.2 - - - +
133F LYS* 1.3 62.2 + - - +
135F SER* 3.7 9.8 + - - -
136F GLU* 3.4 23.6 + - - +
160F GLU* 4.7 4.9 - - - +
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Residues in contact with LYS 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F GLU* 4.9 3.2 + - - -
100F GLN* 3.8 33.9 + - - +
103F HIS* 5.1 10.5 + - - +
125F TYR* 4.1 28.9 + - + -
130F ARG* 3.4 34.7 + - + +
131F LEU 3.3 0.4 - - - -
132F ALA* 1.3 78.4 - - - +
134F GLY* 1.3 61.6 + - - +
136F GLU* 3.3 21.9 + - - +
137F CYS* 3.3 18.9 + - - +
504Y ALA* 3.7 20.6 - - + +
505Y ASN* 4.1 12.8 + - - +
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Residues in contact with GLY 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F GLY* 4.3 1.9 - - - -
125F TYR* 3.6 28.7 - - - -
126F CYS* 4.1 7.0 - - - -
130F ARG 3.0 9.2 + - - -
131F LEU 3.1 4.8 + - - -
133F LYS* 1.3 72.6 - - - +
135F SER* 1.3 60.9 + - - +
137F CYS* 3.0 6.5 + - - +
138F TYR* 2.8 35.7 + - - -
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Residues in contact with SER 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F CYS* 4.5 0.8 - - - -
131F LEU 3.0 16.5 + - - -
132F ALA* 3.9 4.2 - - - -
133F LYS 3.5 0.2 - - - -
134F GLY* 1.3 75.9 - - - +
136F GLU* 1.3 55.4 + - - +
138F TYR* 3.1 14.2 + - - +
139F GLN* 3.0 33.2 + - - +
155F LEU* 4.0 10.3 - - - +
158F ILE* 3.6 17.3 - - - +
160F GLU* 3.4 41.9 - - - +
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Residues in contact with GLU 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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103F HIS* 5.4 8.3 + - + +
132F ALA* 3.4 15.5 - - - +
133F LYS* 3.3 27.1 + - - +
135F SER* 1.3 77.8 - - - +
137F CYS* 1.3 60.3 + - - +
139F GLN* 3.4 14.9 + - - +
140F LYS* 3.3 28.5 + - - +
160F GLU* 5.2 4.9 - - - +
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Residues in contact with CYS 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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103F HIS* 3.9 21.4 - - + -
118F LEU* 2.9 37.5 - - - +
121F LEU* 3.7 25.4 - - - -
122F GLY* 3.6 12.3 - - - -
125F TYR* 4.0 7.9 - - + -
133F LYS 3.3 8.9 + - - +
134F GLY 3.0 13.9 + - - +
136F GLU* 1.3 76.8 - - - +
138F TYR* 1.3 60.8 + - - -
140F LYS* 3.3 17.0 + - - +
141F SER* 3.1 9.9 + - - -
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Residues in contact with TYR 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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119F SER* 3.5 25.1 - - - -
122F GLY* 3.8 3.5 + - - -
123F HIS* 3.1 33.1 + - + +
126F CYS* 3.4 27.4 - - - +
134F GLY 2.8 26.6 + - - -
135F SER* 3.4 11.2 - - - +
137F CYS* 1.3 69.6 - - - +
139F GLN* 1.3 60.8 + - - +
141F SER* 2.3 27.8 + - - -
142F LEU* 3.3 15.2 - - - +
150F SER 4.8 0.2 - - - -
151F PRO* 3.8 33.6 - - + +
154F SER* 3.6 26.0 + - - -
155F LEU* 4.3 13.7 - - + -
158F ILE* 3.8 13.4 - - + +
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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 SER 3.0 15.7 + - - +
136F GLU* 3.7 16.6 - - - +
137F CYS 3.3 0.2 - - - -
138F TYR* 1.3 75.7 - - - +
140F LYS* 1.3 52.8 + - + +
142F LEU* 3.2 9.7 + - - +
143F SER* 2.7 36.7 + - - +
155F LEU* 3.7 25.0 - - + +
160F GLU* 3.9 20.5 + - - +
161F LYS 5.2 2.0 + - - -
162F PRO* 4.8 6.9 - - - +
166F GLN* 4.0 22.6 - - - +
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Residues in contact with LYS 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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102F SER 5.0 1.1 - - - -
103F HIS* 3.8 35.2 - - + -
104F ASP* 3.8 17.4 + - - +
107F VAL* 5.5 4.0 - - + -
118F LEU* 3.7 17.7 - - + -
136F GLU* 3.3 16.8 + - - +
137F CYS 3.4 9.0 - - - +
138F TYR 3.1 0.2 - - - -
139F GLN* 1.3 78.1 - - + +
141F SER* 1.3 63.9 + - - +
143F SER* 3.2 24.5 - - - +
144F LEU* 3.4 15.9 + - + +
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Residues in contact with SER 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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115F CYS* 3.6 28.3 - - - +
118F LEU* 4.3 2.8 - - - +
119F SER* 4.1 17.5 + - - -
137F CYS 3.1 6.5 + - - -
138F TYR* 2.3 33.4 + - - -
140F LYS* 1.3 75.5 - - - +
142F LEU* 1.3 60.2 + - - -
144F LEU* 3.0 25.7 + - - +
145F ASN* 3.8 6.2 + - - +
146F PRO* 4.5 1.7 - - - +
148F LEU* 5.6 3.4 - - - +
151F PRO* 4.2 11.0 - - - +
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Residues in contact with LEU 142 (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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138F TYR 3.3 19.7 + - - +
139F GLN* 3.2 7.0 + - - +
141F SER* 1.3 75.6 - - - +
143F SER* 1.3 62.5 + - - +
144F LEU 3.2 0.7 + - - -
146F PRO* 3.1 49.1 - - + +
148F LEU* 3.7 13.0 - - + +
151F PRO* 3.8 11.7 - - + -
152F PHE* 3.6 50.3 - - + +
155F LEU* 4.0 18.8 - - + -
166F GLN* 4.0 27.8 - - + +
167F THR* 4.6 3.8 - - + -
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Residues in contact with SER 143 (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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139F GLN* 2.7 22.6 + - - +
140F LYS* 3.2 19.2 + - - +
142F LEU* 1.3 76.5 - - - +
144F LEU* 1.3 59.9 + - - +
145F ASN* 4.6 2.8 - - - +
166F GLN* 5.9 0.8 - - - +
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Residues in contact with LEU 144 (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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107F VAL* 4.2 27.6 - - + -
111F GLY 4.6 12.3 - - - +
112F ASP* 5.2 3.6 - - - +
114F ALA 4.4 0.9 - - - -
115F CYS* 3.8 29.4 - - + +
118F LEU* 3.9 17.7 - - + -
140F LYS* 3.4 17.5 + - + +
141F SER 3.0 9.4 + - - +
143F SER* 1.3 82.9 - - - +
145F ASN* 1.3 70.8 + - - +
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Residues in contact with ASN 145 (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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115F CYS* 3.5 33.1 - - - +
116F PHE* 6.0 1.4 - - - -
141F SER 3.8 1.6 + - - +
142F LEU 3.9 1.6 - - - -
143F SER 4.7 2.3 - - - +
144F LEU* 1.3 83.1 - - - +
146F PRO* 1.3 83.4 - - - +
147F PHE* 3.7 21.6 - - + +
148F LEU* 5.2 4.0 - - - +
169F LYS 3.6 9.0 - - - +
170F PHE* 3.7 17.3 - - - +
463F MET* 5.2 0.3 - - - +
11H ALA* 5.7 4.0 - - - +
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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
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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