Contacts of the helix formed by residues 121 - 130 (chain A) in PDB entry 1PJJ
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 GLN 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ILE* 3.6 19.8 - - + +
118A SER* 2.8 51.4 + - - +
120A ASP* 1.3 82.9 - - - +
122A VAL* 1.3 59.4 + - - +
124A PRO* 3.3 11.2 - - + +
125A TYR* 2.9 30.1 + - - +
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Residues in contact with VAL 122 (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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60A ILE* 4.5 12.8 - - + -
68A ARG* 3.5 41.3 - - + +
70A ILE* 4.9 2.5 - - + -
117A ILE* 3.8 12.1 - - + -
118A SER 3.8 3.6 - - - +
119A THR* 3.6 12.8 - - - +
120A ASP 3.4 1.2 - - - -
121A GLN* 1.3 74.6 - - - +
123A LEU* 1.3 76.3 + - + +
125A TYR* 3.1 12.4 + - - +
126A PHE* 3.2 37.1 + - + -
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Residues in contact with LEU 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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119A THR 4.9 0.4 + - - -
120A ASP 4.8 0.6 + - - -
122A VAL* 1.3 84.0 - - + +
124A PRO* 1.3 72.0 - - + +
126A PHE* 3.3 6.9 + - + +
127A LEU* 3.0 33.7 + - + +
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Residues in contact with PRO 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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120A ASP 3.4 17.3 - - - +
121A GLN* 3.3 19.5 - - - +
123A LEU* 1.3 95.9 - - + +
125A TYR* 1.3 55.2 + - - +
127A LEU* 3.2 13.3 + - + +
128A LYS* 2.9 31.2 + - - +
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Residues in contact with TYR 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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58A TYR* 3.5 9.3 - + - -
70A ILE* 3.6 31.4 - - + +
115A GLU* 2.6 27.4 + - + -
117A ILE* 4.0 17.7 - - + -
121A GLN 2.9 19.9 + - - +
122A VAL 3.1 5.8 + - - +
124A PRO* 1.3 78.5 - - - +
126A PHE* 1.3 91.5 + + - +
128A LYS* 3.4 7.5 + - - +
129A LYS* 3.2 48.1 + - + +
1004A GOL 2.6 27.7 + - - -
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Residues in contact with PHE 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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55A ARG* 3.7 42.0 - - + +
58A TYR* 3.5 39.9 - + + -
60A ILE* 3.7 25.6 - - + -
70A ILE* 4.1 7.9 - - + -
122A VAL* 3.2 34.4 + - + -
123A LEU* 4.0 7.9 - - + +
125A TYR* 1.3 100.1 - + - +
127A LEU* 1.3 66.6 + - - +
128A LYS 3.2 0.2 - - - -
129A LYS* 3.2 4.2 + - + +
130A LYS 3.1 15.8 + - - -
131A ILE* 3.5 28.7 + - + +
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Residues in contact with LEU 127 (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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123A LEU* 3.0 27.1 + - + +
124A PRO* 3.6 14.1 - - + +
126A PHE* 1.3 76.9 - - - +
128A LYS* 1.3 63.0 + - - +
130A LYS* 3.0 19.9 + - - +
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Residues in contact with LYS 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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124A PRO 2.9 17.0 + - - +
125A TYR* 3.5 8.7 - - - +
127A LEU* 1.3 78.1 - - - +
129A LYS* 1.3 63.0 + - + +
130A LYS* 3.1 12.2 + - - +
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Residues in contact with LYS 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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58A TYR* 3.8 13.0 - - - +
115A GLU* 5.1 2.2 + - - -
125A TYR* 3.2 56.9 + - + +
126A PHE* 3.6 4.5 - - + +
127A LEU 3.2 0.6 - - - -
128A LYS* 1.3 77.4 - - + +
130A LYS* 1.3 69.8 + - - +
131A ILE* 3.2 29.1 + - + +
164A THR* 5.6 0.7 - - - +
1004A GOL 3.4 16.3 + - - -
10D T 2.8 36.9 + - - +
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Residues in contact with LYS 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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126A PHE 3.1 1.7 + - - -
127A LEU* 3.0 19.6 + - - +
128A LYS 3.8 11.0 - - - +
129A LYS* 1.3 80.7 - - - +
131A ILE* 1.3 65.1 + - - +
132A GLY* 3.4 2.3 + - - -
163A GLN 4.7 0.2 - - - -
164A THR* 3.7 28.1 - - + +
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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