Contacts of the helix formed by residues 108 - 126 (chain A) in PDB entry 1PR9
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 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PHE* 3.3 30.8 + - + +
106A VAL 3.3 0.4 - - - -
107A ASN* 1.3 81.2 - - + +
109A ARG* 1.3 68.0 + - - +
110A ALA 3.2 1.3 - - - -
111A VAL* 3.0 14.6 + - - +
112A ILE* 3.2 21.1 + - + +
152A THR* 4.2 3.4 - - - +
155A ALA* 3.7 23.3 - - + +
156A LEU* 3.8 38.4 - - + +
159A LEU* 3.8 23.3 - - + -
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Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLY 3.1 27.3 + - - -
64A TRP* 3.8 49.1 - - + +
104A PHE 2.9 16.8 + - - +
105A GLU* 3.5 39.7 + - + +
108A LEU* 1.3 72.5 - - - +
110A ALA* 1.3 61.3 + - - +
112A ILE* 3.2 15.4 + - + +
113A GLN* 3.1 21.5 + - - +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.6 43.7 - - + +
64A TRP* 6.0 0.2 - - - -
67A THR* 6.2 0.4 - - + -
82A ASN* 5.4 0.2 - - - -
105A GLU 3.0 8.4 + - - +
106A VAL 3.4 20.0 - - - +
108A LEU 3.2 0.6 - - - -
109A ARG* 1.3 73.6 - - - +
111A VAL* 1.3 65.7 + - + +
113A GLN* 4.4 8.3 - - - +
114A VAL* 2.9 31.5 + - + +
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASN* 3.8 26.9 + - + +
84A ALA 5.5 4.3 - - - +
106A VAL 4.7 3.1 - - - +
107A ASN 3.5 25.1 - - - +
108A LEU* 3.0 9.1 + - - +
110A ALA* 1.3 78.1 - - + +
112A ILE* 1.3 61.7 + - - +
115A SER* 2.7 35.0 + - - +
133A ASN* 3.7 24.7 - - - +
156A LEU* 3.9 15.0 - - + -
159A LEU* 3.8 20.0 - - + -
163A MET* 4.9 1.6 - - - -
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP* 5.0 7.4 - - + -
108A LEU* 3.2 20.7 + - + +
109A ARG* 3.5 14.6 - - + +
111A VAL* 1.3 78.5 - - - +
113A GLN* 1.3 64.4 + - - +
115A SER* 3.8 3.5 - - - -
116A GLN* 2.9 48.1 + - + +
159A LEU* 3.9 31.6 - - + -
163A MET* 5.8 2.0 - - - -
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU 5.1 2.3 - - - +
64A TRP* 3.0 75.1 + - + +
67A THR* 3.5 25.2 - - + +
68A GLU* 3.6 19.8 + - - +
109A ARG 3.1 11.7 + - - +
110A ALA* 3.3 7.9 + - - +
112A ILE* 1.3 78.3 - - - +
114A VAL* 1.3 64.6 + - + +
116A GLN* 3.3 13.8 + - - +
117A ILE* 3.2 31.9 + - + +
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.2 11.0 - - + -
13A THR* 4.4 7.4 - - + -
61A LEU* 4.2 18.6 - - + -
67A THR* 4.3 6.5 - - + -
71A LEU* 3.8 31.0 - - + -
80A LEU* 3.8 27.1 - - + -
82A ASN* 4.1 9.4 - - - +
110A ALA* 2.9 18.0 + - + +
113A GLN* 1.3 75.2 - - + +
115A SER* 1.3 62.7 + - - +
117A ILE* 3.2 10.5 + - + +
118A VAL* 3.1 24.9 + - + +
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.7 12.8 - - - +
82A ASN* 3.1 21.5 + - - -
111A VAL* 2.7 24.5 + - - +
112A ILE* 3.8 3.6 - - - -
114A VAL* 1.3 77.2 - - - +
116A GLN* 1.3 56.5 + - - +
118A VAL* 4.0 0.2 - - - +
119A ALA* 2.7 34.1 + - - +
131A ILE* 4.2 5.5 - - - +
163A MET* 3.6 30.5 - - - +
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP* 4.0 16.4 - - - -
112A ILE* 2.9 33.5 + - + +
113A GLN* 3.5 18.1 - - - +
114A VAL 3.3 0.2 - - - -
115A SER* 1.3 75.4 - - - +
117A ILE* 1.3 58.8 + - - +
119A ALA* 4.6 4.0 - - - -
120A ARG* 2.8 73.1 + - - +
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 6.4 0.9 - - + -
67A THR* 5.0 0.7 - - + +
68A GLU* 4.8 15.3 - - + -
71A LEU* 3.9 45.3 - - + +
72A GLY* 4.9 8.5 - - - +
74A VAL* 5.0 7.9 - - + -
113A GLN* 3.2 29.8 + - + +
114A VAL* 3.2 11.9 + - + +
116A GLN* 1.3 82.8 - - - +
118A VAL* 1.3 66.4 + - + +
120A ARG* 3.9 18.8 - - - +
121A GLY* 3.4 15.8 + - - -
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.7 7.4 - - + -
74A VAL* 6.3 0.9 - - + -
77A VAL* 3.8 45.6 - - + +
78A ASP 5.1 2.0 - - - -
79A LEU 5.2 0.2 - - - -
80A LEU* 3.8 33.2 - - + -
114A VAL* 3.1 20.6 + - + +
115A SER 4.0 2.5 - - - +
117A ILE* 1.3 79.3 - - + +
119A ALA* 1.3 65.3 + - - +
121A GLY* 3.4 2.6 + - - -
122A LEU* 3.1 33.6 + - + +
130A ALA 6.1 0.2 - - - +
131A ILE* 5.2 5.4 - - + -
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER 2.7 22.5 + - - +
116A GLN* 4.1 4.0 - - - +
118A VAL* 1.3 70.1 - - - +
120A ARG* 1.3 65.5 + - - +
122A LEU* 3.2 10.1 + - - +
123A ILE* 3.0 31.1 + - + +
131A ILE* 5.1 4.7 - - + +
167A LEU* 4.4 33.0 - - + -
172A ILE* 4.5 8.5 - - + -
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN* 2.8 66.0 + - - +
117A ILE* 3.9 18.1 - - - +
119A ALA* 1.3 77.9 - - + +
121A GLY* 1.3 56.4 + - - +
123A ILE* 3.3 10.0 + - + +
124A ALA* 3.0 28.3 + - - +
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Residues in contact with GLY 121 (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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117A ILE 3.4 7.5 + - - -
118A VAL 3.4 5.1 + - - -
119A ALA 3.3 0.4 - - - -
120A ARG* 1.3 76.1 - - - +
122A LEU* 1.3 66.2 + - - +
124A ALA* 3.3 6.1 + - - +
125A ARG* 3.0 37.0 + - - +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL 3.6 8.7 - - - +
78A ASP* 3.8 21.8 - - - +
118A VAL* 3.1 30.6 + - + +
119A ALA* 3.2 7.4 + - - +
121A GLY* 1.3 76.1 - - - +
123A ILE* 1.3 58.0 - - - +
125A ARG* 3.0 30.5 + - - +
126A GLY 2.9 21.5 + - - -
127A VAL* 3.0 38.8 + - + +
128A PRO 3.9 10.1 - - - +
129A GLY* 4.0 14.8 - - - -
130A ALA 4.8 0.9 - - - +
131A ILE* 5.9 2.5 - - + -
172A ILE* 4.2 22.0 - - + -
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Residues in contact with ILE 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 ALA* 3.0 24.3 + - + +
120A ARG* 3.8 6.3 - - - +
122A LEU* 1.3 74.8 - - - +
124A ALA* 1.3 66.8 + - - +
126A GLY* 3.1 14.3 + - - +
127A VAL 5.4 0.4 - - - -
167A LEU* 4.8 8.5 - - + -
170A HIS* 3.5 59.9 - - + +
172A ILE* 4.2 9.0 - - + -
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Residues in contact with ALA 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 ARG 3.0 17.6 + - - +
121A GLY* 3.6 8.1 - - - +
122A LEU 3.3 0.4 - - - -
123A ILE* 1.3 80.3 - - - +
125A ARG* 1.3 62.3 + - + +
126A GLY* 3.1 1.1 + - - -
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PRO* 4.0 29.4 - - - +
77A VAL 3.0 34.8 + - - +
78A ASP* 3.4 16.2 + - - -
121A GLY* 3.0 18.9 + - - +
122A LEU* 3.0 29.2 - - - +
124A ALA* 1.3 79.0 - - + +
126A GLY* 1.3 62.7 + - - +
127A VAL* 3.4 24.2 + - + +
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Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU 2.9 4.5 + - - -
123A ILE* 3.1 15.5 + - - -
124A ALA 3.1 1.2 + - - -
125A ARG* 1.3 78.7 - - - +
127A VAL* 1.3 61.2 + - - +
128A PRO* 4.6 1.0 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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