Contacts of the helix formed by residues 122 - 132 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.5 34.8 - - + +
33A PHE* 3.5 35.0 - - + -
73A PHE* 4.6 5.6 - - + -
95A ALA* 5.4 2.7 - - + +
96A ASN* 3.1 12.1 - - - +
99A LEU* 3.7 20.3 - - + +
115A THR* 5.3 2.7 - - + -
117A GLY* 3.6 18.8 - - - -
118A GLY* 3.9 5.4 - - - -
119A ASP 3.2 18.4 - - - +
120A HIS 4.7 0.2 - - - -
121A SER* 1.3 76.2 + - - +
123A ALA* 1.3 65.1 + - - +
124A ILE 3.0 0.2 - - - -
125A GLY* 2.9 13.3 + - - -
126A THR* 3.1 16.8 + - + +
295A VAL* 4.9 5.8 - - + -
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A HIS* 3.1 34.6 + - + +
121A SER 3.0 0.8 - - - -
122A LEU* 1.3 78.7 - - - +
124A ILE* 1.3 64.1 - - - +
126A THR* 3.3 11.8 + - - +
127A ILE* 2.9 31.6 + - + +
141A TRP* 3.6 23.6 - - + -
163A PRO* 4.3 2.9 - - + -
167A LEU* 4.2 2.0 - - + +
249A SER* 4.2 4.7 - - - +
293A ASP* 4.4 3.3 - - - +
295A VAL* 5.8 1.0 - - - +
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A VAL* 5.0 2.9 - - + -
96A ASN* 3.7 16.8 - - - +
121A SER* 3.0 19.0 + - - +
122A LEU 3.0 0.8 - - - -
123A ALA* 1.3 78.6 - - - +
125A GLY* 1.3 58.2 + - - +
128A SER* 2.9 36.8 + - - +
159A LEU* 5.5 2.2 - - + +
163A PRO* 4.0 24.4 - - + +
166A PHE* 3.7 29.2 - - + -
167A LEU* 4.0 13.2 - - + +
181A PHE* 3.9 17.7 - - + -
183A TRP* 4.3 5.4 - - + -
184A ILE* 3.4 33.2 - - + -
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASN* 2.8 42.9 + - - -
99A LEU* 4.5 2.5 - - - -
100A ALA* 3.4 17.4 - - - +
122A LEU 2.9 2.3 + - - -
124A ILE* 1.3 74.0 - - - +
126A THR* 1.3 53.6 + - - -
128A SER* 3.2 1.4 + - - -
129A GLY* 2.8 31.2 + - - -
183A TRP* 4.4 1.1 - - - -
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.6 19.0 - - + +
103A VAL* 3.6 16.2 - - + +
115A THR* 3.5 23.8 - - + +
122A LEU* 3.1 13.2 + - + +
123A ALA* 3.3 10.4 + - - -
125A GLY* 1.3 73.8 - - - +
127A ILE* 1.3 60.3 + - - +
130A HIS* 2.9 31.2 + - - +
247A HIS* 3.5 7.4 + - - -
291A ALA* 6.2 0.2 - - - -
293A ASP* 3.0 39.5 + - - +
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA* 2.9 19.7 + - + +
126A THR* 1.3 74.4 + - - +
128A SER* 1.3 61.9 + - - +
130A HIS* 3.9 2.4 - - - +
131A ALA* 2.9 28.4 + - - +
137A LEU* 4.3 10.7 - - + +
139A VAL* 4.1 20.6 - - + -
141A TRP* 4.0 22.4 - - + -
167A LEU* 3.4 34.8 - - + -
187A CYS* 4.5 9.4 - - - -
188A ILE* 4.6 9.4 - - + -
247A HIS* 3.3 35.4 - - + +
293A ASP* 4.6 0.4 - - - +
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ALA* 4.3 1.1 - - - -
124A ILE* 2.9 25.9 + - - +
125A GLY 3.5 3.8 - - - -
127A ILE* 1.3 79.0 - - - +
129A GLY* 1.3 63.9 + - - +
131A ALA* 3.2 2.4 + - - +
132A ARG* 3.0 27.9 + - - +
167A LEU* 4.2 10.4 - - - +
183A TRP* 3.8 28.7 - - - -
184A ILE* 4.6 6.4 - - - +
185A LYS 5.2 3.3 + - - -
187A CYS* 4.6 11.3 - - - -
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ALA* 3.1 29.5 - - - +
103A VAL* 4.1 1.6 - - - -
104A SER* 3.0 32.2 - - - -
107A VAL* 5.0 0.3 - - - +
125A GLY 2.8 18.0 + - - -
126A THR 4.0 0.4 - - - -
128A SER* 1.3 73.2 - - - +
130A HIS* 1.3 59.5 + - - +
132A ARG* 3.1 12.2 - - - +
133A HIS* 4.1 1.6 + - - -
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Residues in contact with HIS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A VAL* 3.9 6.0 - - + +
107A VAL* 4.0 20.2 - - + -
126A THR 2.9 20.8 + - - +
127A ILE* 3.9 2.9 - - - +
128A SER 3.2 0.2 - - - -
129A GLY* 1.3 72.2 - - - +
131A ALA* 1.3 67.2 + - - +
132A ARG 3.0 1.3 - - - -
133A HIS* 3.0 6.8 + - - +
134A CYS* 3.0 36.3 + - + +
137A LEU* 3.6 18.7 - - + +
245A PRO* 4.2 0.8 - - + +
246A ILE 4.2 6.3 - - - -
247A HIS* 2.9 27.3 + - + +
290A SER* 3.1 36.5 + - - -
291A ALA* 3.5 14.1 - - + +
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ILE* 2.9 20.5 + - + +
128A SER 3.7 3.6 - - - +
130A HIS* 1.3 76.0 - - - +
132A ARG* 1.3 63.7 + - - +
133A HIS 2.9 1.8 + - - -
134A CYS 3.7 5.8 - - - +
135A PRO* 3.1 30.1 - - + +
137A LEU* 3.5 20.5 - - + +
187A CYS* 4.0 27.6 - - + -
188A ILE* 5.5 1.3 - - + -
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLN* 6.2 0.8 - - - +
100A ALA* 3.6 35.1 + - - +
101A GLU* 3.6 24.7 + - - +
104A SER* 4.0 16.4 + - - +
128A SER* 3.0 15.9 + - - +
129A GLY* 3.1 19.3 - - - +
131A ALA* 1.3 77.1 - - - +
133A HIS* 1.3 67.5 + - + +
135A PRO* 4.9 4.0 - - - +
183A TRP* 4.5 17.0 - - - -
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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