Contacts of the helix formed by residues 122 - 134 (chain F) in PDB entry 1PQ3
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 LEU 122 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F ALA* 3.6 27.6 - - + +
33F PHE* 3.4 38.4 - - + -
73F PHE* 4.7 5.4 - - + -
95F ALA* 5.4 2.5 - - + -
96F ASN* 3.2 12.3 - - - +
99F LEU* 3.6 15.3 - - + +
115F THR* 5.1 3.8 - - + -
117F GLY* 3.6 28.7 - - - -
118F GLY* 3.9 5.6 - - - -
119F ASP 3.1 19.5 - - - +
120F HIS* 3.0 0.6 - - - -
121F SER* 1.3 77.8 + - - +
123F ALA* 1.3 60.2 + - - +
124F ILE 3.0 0.7 - - - -
125F GLY 3.1 3.3 + - - -
126F THR* 3.0 27.4 + - + +
293F ASP* 6.0 0.4 - - - -
295F VAL* 5.0 5.4 - - + -
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Residues in contact with ALA 123 (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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120F HIS* 3.2 25.1 + - + +
121F SER 3.0 0.8 - - - -
122F LEU* 1.3 75.8 - - - +
124F ILE* 1.3 65.4 + - - +
126F THR* 3.3 11.7 - - - +
127F ILE* 3.0 32.2 + - + +
141F TRP* 3.7 28.5 - - + -
163F PRO* 4.4 2.5 - - + -
167F LEU* 4.0 2.8 - - + +
249F SER* 4.0 8.1 - - - +
293F ASP* 4.4 3.4 - - - +
295F VAL* 5.9 0.6 - - - +
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Residues in contact with ILE 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F VAL* 4.8 3.8 - - + -
96F ASN* 3.7 15.9 - - + +
121F SER* 3.0 21.6 + - - +
123F ALA* 1.3 78.9 - - - +
125F GLY* 1.3 57.3 + - - +
128F SER* 2.5 37.4 + - - +
159F LEU* 5.4 2.9 - - + +
163F PRO* 4.0 24.2 - - + +
166F PHE* 3.7 27.8 - - + -
167F LEU* 4.1 12.8 - - + +
181F PHE* 3.8 17.3 - - + -
183F TRP* 4.6 0.7 - - + -
184F ILE* 3.3 36.3 - - + -
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Residues in contact with GLY 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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96F ASN* 2.6 44.3 + - - -
99F LEU* 4.6 2.7 - - - -
100F ALA* 3.6 15.5 - - - -
122F LEU 3.6 0.2 - - - -
124F ILE* 1.3 74.3 - - - +
126F THR* 1.3 60.4 + - - +
128F SER* 3.1 2.3 + - - -
129F GLY 2.8 27.2 + - - -
183F TRP* 4.4 1.6 - - - -
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Residues in contact with THR 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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99F LEU* 3.5 17.9 - - + +
103F VAL* 3.7 18.0 - - + +
115F THR* 3.3 29.6 - - + +
122F LEU* 3.0 12.3 + - + +
123F ALA* 3.3 12.1 - - - -
125F GLY* 1.3 73.2 - - - +
127F ILE* 1.3 58.7 + - - +
130F HIS* 3.0 29.5 + - - +
247F HIS* 3.7 7.9 + - - -
291F ALA* 6.1 0.2 - - - -
293F ASP* 3.1 33.3 + - - +
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Residues in contact with ILE 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F ALA* 3.0 16.5 + - + +
126F THR* 1.3 77.9 + - - +
128F SER* 1.3 60.0 + - - +
130F HIS* 3.8 2.6 - - - +
131F ALA* 2.8 27.2 + - - +
137F LEU* 4.2 15.7 - - + +
139F VAL* 4.2 15.3 - - + -
141F TRP* 4.0 20.6 - - + -
167F LEU* 3.5 35.0 - - + -
187F CYS* 4.5 9.6 - - - -
188F ILE* 4.6 10.1 - - + -
247F HIS* 3.3 35.9 - - + +
293F ASP* 4.7 0.4 - - - +
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Residues in contact with SER 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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100F ALA* 4.5 0.4 - - - -
124F ILE* 2.5 26.5 + - - +
125F GLY 3.1 3.3 + - - -
127F ILE* 1.3 76.8 - - - +
129F GLY* 1.3 64.7 + - - +
131F ALA* 3.3 6.0 + - - +
132F ARG* 3.0 29.7 + - - +
167F LEU* 3.9 12.5 - - - +
183F TRP* 4.0 24.9 - - - -
184F ILE* 4.7 7.7 - - - +
185F LYS 5.5 2.4 + - - -
187F CYS* 4.9 6.1 - - - -
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Residues in contact with GLY 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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100F ALA* 3.2 29.5 - - - +
103F VAL* 4.5 1.6 - - - -
104F SER* 3.1 22.5 - - - -
125F GLY 2.8 13.6 + - - -
126F THR 4.1 0.9 - - - -
128F SER* 1.3 78.3 - - - +
130F HIS* 1.3 60.7 + - - +
132F ARG* 3.0 20.9 - - - +
133F HIS* 3.9 1.6 + - - +
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Residues in contact with HIS 130 (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 VAL* 3.9 9.5 - - + +
107F VAL* 4.0 23.8 - - + +
126F THR 3.0 20.2 + - - +
127F ILE 3.8 1.1 - - - +
129F GLY* 1.3 73.2 - - - +
131F ALA* 1.3 65.6 + - - +
133F HIS* 3.1 6.2 + - - +
134F CYS* 3.0 31.6 + - - +
137F LEU* 3.4 23.9 - - + +
245F PRO* 4.2 1.1 - - + +
246F ILE 4.2 7.2 - - - -
247F HIS* 3.0 26.5 + - + +
290F SER* 2.9 38.4 + - - -
291F ALA* 3.5 13.5 - - + +
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Residues in contact with ALA 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 ILE* 2.8 24.0 + - + +
128F SER 3.7 4.0 - - - +
130F HIS* 1.3 73.0 - - - +
132F ARG* 1.3 63.1 + - - +
133F HIS 3.0 1.6 + - - -
134F CYS 3.8 5.4 - - - +
135F PRO* 3.2 28.6 - - + +
137F LEU* 3.6 18.5 - - + +
187F CYS* 4.0 29.2 - - + -
188F ILE* 5.3 1.6 - - + -
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Residues in contact with ARG 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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97F GLN* 5.8 1.0 - - - +
100F ALA* 3.8 24.9 + - - +
101F GLU* 3.9 21.4 + - - +
104F SER* 4.0 17.8 + - - -
128F SER* 3.0 16.0 + - - +
129F GLY* 3.0 17.3 - - - +
130F HIS 3.1 0.2 - - - -
131F ALA* 1.3 76.8 - - - +
133F HIS* 1.3 56.4 + - - +
135F PRO* 4.7 4.7 - - - +
183F TRP* 3.8 31.9 + - - -
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Residues in contact with HIS 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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104F SER* 5.2 4.7 - - - +
107F VAL* 4.0 29.9 + - + -
108F SER* 4.0 27.7 + - - +
129F GLY 3.9 2.0 + - - +
130F HIS 3.1 3.2 + - - +
131F ALA 3.1 0.2 - - - -
132F ARG* 1.3 75.7 - - - +
134F CYS* 1.3 73.7 + - - +
135F PRO* 2.9 17.2 - - - +
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Residues in contact with CYS 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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107F VAL* 4.0 12.1 - - - -
130F HIS* 3.0 27.6 + - - +
131F ALA* 3.4 5.4 - - - +
133F HIS* 1.3 95.1 - - - +
135F PRO* 1.3 56.1 - - - +
136F ASP 3.1 5.6 - - - -
137F LEU* 3.0 27.8 + - + +
245F PRO* 3.7 32.3 - - + -
290F SER* 4.7 3.6 - - - -
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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
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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