Contacts of the helix formed by residues 108 - 126 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B PHE* 3.2 30.8 + - + +
106B VAL 3.3 1.0 - - - -
107B ASN* 1.3 80.7 - - + +
109B ARG* 1.3 67.2 + - - +
110B ALA 3.2 1.3 - - - -
111B VAL* 3.0 15.5 + - - +
112B ILE* 3.1 21.7 + - + +
152B THR* 4.1 5.4 - - - +
155B ALA* 3.7 24.7 - - + +
156B LEU* 3.8 37.9 - - + +
159B LEU* 3.8 20.4 - - + -
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Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY 3.1 26.7 + - - -
64B TRP* 3.8 47.3 - - + +
104B PHE 3.0 14.1 + - - +
105B GLU* 3.6 42.0 + - - +
108B LEU* 1.3 75.5 - - - +
110B ALA* 1.3 60.4 + - - +
112B ILE* 3.1 15.4 + - + +
113B GLN* 3.0 26.0 + - - +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.5 44.6 - - + +
64B TRP* 6.0 0.2 - - - -
67B THR* 6.3 0.4 - - + -
82B ASN* 5.4 0.2 - - - -
84B ALA* 6.5 0.4 - - + -
105B GLU 3.1 8.9 + - - +
106B VAL 3.3 19.5 - - - +
108B LEU 3.2 0.2 - - - -
109B ARG* 1.3 75.9 - - - +
111B VAL* 1.3 64.2 + - + +
113B GLN* 4.3 8.5 - - - +
114B VAL* 3.0 31.0 + - + +
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASN* 3.7 37.8 + - + +
84B ALA 5.5 4.5 - - - +
106B VAL 4.7 2.9 - - - +
107B ASN* 3.4 26.2 - - - +
108B LEU 3.0 9.2 + - - +
110B ALA* 1.3 78.0 - - + +
112B ILE* 1.3 64.3 + - - +
115B SER* 2.7 32.7 + - - +
133B ASN* 3.8 13.5 - - - +
156B LEU* 3.9 24.2 - - + -
159B LEU* 3.9 11.0 - - + -
163B MET* 4.9 1.3 - - - -
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B TRP* 5.0 8.1 - - + -
108B LEU* 3.1 20.5 + - + +
109B ARG* 3.1 15.9 + - + +
111B VAL* 1.3 78.9 - - - +
113B GLN* 1.3 65.4 + - - +
115B SER* 3.8 3.6 - - - -
116B GLN* 2.9 47.8 + - + +
159B LEU* 3.9 29.4 - - + -
163B MET* 5.9 1.8 - - - -
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU 5.0 3.5 - - - +
64B TRP* 2.9 74.6 + - + +
67B THR* 3.3 30.3 - - + +
68B GLU* 3.6 20.8 + - - +
109B ARG 3.0 11.7 + - - +
110B ALA* 3.3 6.9 + - - +
112B ILE* 1.3 79.4 - - - +
114B VAL* 1.3 65.0 + - + +
116B GLN* 3.2 13.0 + - - +
117B ILE* 3.2 27.9 + - + +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.4 8.5 - - + -
13B THR* 4.5 7.6 - - + -
61B LEU* 4.1 19.7 - - + -
67B THR* 4.5 6.5 - - + -
71B LEU* 4.0 30.1 - - + -
80B LEU* 3.8 27.1 - - + -
82B ASN* 4.0 8.1 - - - +
110B ALA* 3.0 18.1 + - + +
113B GLN* 1.3 75.5 - - + +
115B SER* 1.3 62.9 + - - +
117B ILE* 3.1 10.8 + - + +
118B VAL* 3.0 25.5 + - + +
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.7 13.6 - - - +
82B ASN* 3.1 21.5 + - - -
111B VAL* 2.7 24.2 + - - +
112B ILE* 3.8 2.9 - - - -
114B VAL* 1.3 74.8 - - - +
116B GLN* 1.3 56.4 + - - +
118B VAL* 3.3 0.9 + - - +
119B ALA* 2.7 39.0 + - - +
131B ILE* 4.3 4.8 - - - +
163B MET* 3.4 30.6 - - - +
167B LEU* 6.0 0.4 - - - -
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Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TRP* 4.1 15.9 - - - -
112B ILE* 2.9 37.5 + - + +
113B GLN* 3.6 15.1 - - - +
115B SER* 1.3 76.2 - - - +
117B ILE* 1.3 59.7 + - - +
119B ALA* 4.0 4.2 - - - +
120B ARG* 2.8 69.5 + - + +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 6.4 0.7 - - + -
67B THR* 5.0 1.1 - - + +
68B GLU* 4.7 13.5 - - + -
71B LEU* 4.0 40.4 - - + +
72B GLY* 4.6 13.5 - - - +
74B VAL* 4.7 11.2 - - + -
113B GLN* 3.2 27.5 + - + +
114B VAL* 3.1 11.7 + - + +
116B GLN* 1.3 81.4 - - - +
118B VAL* 1.3 67.3 + - + +
120B ARG* 3.6 20.4 + - - +
121B GLY* 3.4 14.7 + - - -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.6 10.3 - - + -
74B VAL* 5.9 0.4 - - + -
77B VAL* 3.9 49.3 - - + +
78B ASP 5.2 0.7 - - - -
79B LEU* 5.2 1.8 - - - -
80B LEU* 4.2 32.1 - - + -
114B VAL* 3.0 17.4 + - + +
115B SER 3.9 1.8 - - - +
117B ILE* 1.3 81.6 - - + +
119B ALA* 1.3 62.7 + - - +
121B GLY* 3.2 3.6 + - - -
122B LEU* 3.1 31.9 + - + +
130B ALA 6.1 0.2 - - - +
131B ILE* 5.4 5.2 - - + -
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER 2.7 23.4 + - - +
116B GLN* 4.0 4.3 - - - +
118B VAL* 1.3 74.9 - - - +
120B ARG* 1.3 62.4 + - - +
122B LEU* 3.2 4.8 + - - +
123B ILE* 3.1 30.4 + - + +
131B ILE* 5.1 3.8 - - + +
167B LEU* 4.2 25.4 - - + -
172B ILE* 4.2 21.7 - - + +
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLU* 5.7 2.6 + - - -
113B GLN 5.4 0.2 + - - -
116B GLN* 2.8 64.8 + - - +
117B ILE* 4.0 18.4 - - - +
119B ALA* 1.3 71.2 - - - +
121B GLY* 1.3 58.8 + - - +
123B ILE* 3.4 8.8 + - - +
124B ALA* 3.0 28.6 + - - +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLY 5.9 3.4 - - - -
76B PRO* 6.3 1.6 - - - -
77B VAL 5.7 0.9 - - - -
117B ILE 3.4 7.8 + - - -
118B VAL 3.2 7.4 + - - -
119B ALA 3.2 0.6 - - - -
120B ARG* 1.3 79.2 - - - +
122B LEU* 1.3 62.1 + - - +
124B ALA* 3.5 5.8 + - - +
125B ARG* 3.1 37.1 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL 3.6 20.2 - - - +
78B ASP* 4.0 13.0 - - - +
118B VAL* 3.1 31.6 + - + +
119B ALA* 3.2 6.0 + - - +
121B GLY* 1.3 76.8 - - - +
123B ILE* 1.3 58.3 + - - +
125B ARG* 3.2 7.9 + - - +
126B GLY 2.9 22.5 + - - -
127B VAL* 3.2 44.9 + - + +
128B PRO 3.8 10.8 - - - +
129B GLY* 4.0 16.8 - - - -
130B ALA 4.8 0.9 - - - +
131B ILE* 5.8 1.8 - - + -
172B ILE* 3.8 30.1 - - + -
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 3.1 25.9 + - + +
120B ARG* 3.8 7.4 - - + +
122B LEU* 1.3 74.6 - - - +
124B ALA* 1.3 62.0 + - - +
126B GLY* 2.9 20.1 + - - +
167B LEU* 5.0 6.5 - - + -
170B HIS* 3.7 54.3 - - + +
172B ILE* 4.4 7.2 - - + -
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ARG 3.0 18.3 + - - +
121B GLY* 3.9 7.4 - - - +
122B LEU 3.3 0.2 - - - -
123B ILE* 1.3 80.6 - - - +
125B ARG* 1.3 61.9 + - + +
126B GLY 3.5 0.2 + - - -
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PRO* 3.9 22.9 - - - +
77B VAL 3.6 28.5 + - - +
78B ASP* 2.7 29.7 + - - -
121B GLY* 3.1 22.0 + - - +
122B LEU* 3.8 14.8 - - - +
123B ILE 3.1 0.6 - - - -
124B ALA* 1.3 81.2 - - + +
126B GLY* 1.3 64.0 + - - +
127B VAL* 3.5 29.2 + - + +
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Residues in contact with GLY 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LEU 2.9 5.7 + - - -
123B ILE* 2.9 15.2 + - - -
124B ALA 3.2 0.4 + - - -
125B ARG* 1.3 80.3 - - - +
127B VAL* 1.3 61.6 + - - +
128B PRO* 4.7 0.3 - - - +
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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