Contacts of the helix formed by residues 103 - 117 (chain B) in PDB entry 1PM9
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 SER 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ILE* 3.7 8.1 - - - +
98B LYS* 4.1 12.1 - - - -
101B PHE* 3.4 3.7 + - - +
102B GLY* 1.3 77.8 - - - +
104B PHE* 1.3 63.8 - - - +
105B ASP* 3.6 8.0 + - - +
106B LYS* 3.2 29.6 + - - +
107B PHE* 3.1 21.5 + - - +
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Residues in contact with PHE 104 (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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87B GLY 4.1 5.4 - - - -
88B GLU* 3.9 35.9 - - + +
89B PRO* 3.4 39.3 - - + -
94B LEU* 4.2 8.5 - - + -
97B ILE* 3.8 12.3 - - + +
98B LYS* 4.6 4.4 - - - +
103B SER* 1.3 72.4 - - - +
105B ASP* 1.3 66.8 + - - +
107B PHE* 3.1 25.3 + + - +
108B LYS* 2.9 62.7 + - + +
181B TRP* 4.7 2.9 - + + -
186B TRP* 3.6 27.8 - + - -
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Residues in contact with ASP 105 (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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103B SER* 3.3 7.4 + - - +
104B PHE* 1.3 85.8 - - - +
106B LYS* 1.3 61.8 + - + +
108B LYS* 3.3 27.9 + - - +
109B GLU* 3.0 38.2 + - - +
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Residues in contact with LYS 106 (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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101B PHE* 3.3 26.7 + - - +
102B GLY* 4.2 8.7 - - - -
103B SER* 3.2 24.3 + - - +
105B ASP* 1.3 74.9 - - + +
107B PHE* 1.3 59.7 + - - +
109B GLU* 3.3 13.9 + - - +
110B LYS* 2.9 43.0 + - + +
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Residues in contact with PHE 107 (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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97B ILE* 3.4 28.5 - - + -
101B PHE* 3.7 31.8 - + + +
103B SER 3.1 5.8 + - - +
104B PHE* 3.3 27.6 - + - +
106B LYS* 1.3 74.6 - - - +
108B LYS* 1.3 67.0 + - - +
110B LYS* 3.1 4.6 + - - +
111B LEU* 2.9 48.1 + - + +
126B LEU* 3.7 42.2 - - + -
137B ILE* 4.3 5.8 - - + -
156B LEU* 4.5 0.4 - - + -
181B TRP* 3.8 11.4 - + - -
186B TRP* 3.8 26.9 - + - -
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Residues in contact with LYS 108 (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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104B PHE* 2.9 59.8 + - + +
105B ASP* 3.5 21.4 + - - +
107B PHE* 1.3 76.9 - - - +
109B GLU* 1.3 57.7 + - + +
111B LEU 3.3 0.2 + - - -
112B THR* 2.8 36.4 + - - -
181B TRP* 3.7 53.5 - - + +
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Residues in contact with GLU 109 (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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105B ASP* 3.0 28.9 + - - +
106B LYS* 3.6 15.2 - - - +
108B LYS* 1.3 76.2 - - + +
110B LYS* 1.3 59.0 + - + +
112B THR* 3.4 6.3 + - - +
113B ALA* 3.0 30.0 + - - +
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Residues in contact with LYS 110 (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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100B ASP 5.9 0.2 + - - -
101B PHE* 4.5 24.2 + - + +
106B LYS* 2.9 27.0 + - - +
107B PHE* 3.1 4.9 + - - +
109B GLU* 1.3 77.8 - - + +
111B LEU* 1.3 63.2 + - - +
113B ALA* 3.2 8.1 + - + +
114B ALA* 3.0 22.9 + - - +
137B ILE* 3.3 24.3 - - + +
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Residues in contact with LEU 111 (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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107B PHE* 2.9 36.4 + - + +
108B LYS 4.0 2.5 - - - +
110B LYS* 1.3 71.0 - - - +
112B THR* 1.3 62.6 + - - +
114B ALA* 3.5 1.1 + - + -
115B SER* 2.7 40.1 + - - +
124B GLY* 4.0 2.2 - - - -
125B TRP* 3.7 35.7 - - - +
126B LEU* 4.4 8.5 - - + +
137B ILE* 3.5 19.3 - - + +
156B LEU* 4.0 14.6 - - + +
158B ILE* 3.7 27.6 - - + -
181B TRP* 3.9 17.7 - - + -
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Residues in contact with THR 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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108B LYS 2.8 24.7 + - - -
109B GLU* 3.6 7.0 - - - +
111B LEU* 1.3 78.0 - - - +
113B ALA* 1.3 58.5 + - - +
115B SER* 3.4 0.9 + - - -
116B VAL* 2.8 49.8 + - + +
174B PRO* 5.7 2.9 - - + +
177B LEU* 3.7 23.2 - - + +
181B TRP* 3.5 22.5 + - - -
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Residues in contact with ALA 113 (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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109B GLU 3.0 18.1 + - - +
110B LYS* 3.2 7.4 + - + +
112B THR* 1.3 76.2 - - - +
114B ALA* 1.3 59.8 + - - +
116B VAL* 4.2 3.4 - - - +
117B GLY* 2.9 28.6 + - - -
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Residues in contact with ALA 114 (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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110B LYS 3.0 11.1 + - - +
111B LEU* 3.8 5.2 - - + +
113B ALA* 1.3 77.6 - - - +
115B SER* 1.3 62.5 + - - +
117B GLY* 3.6 5.2 + - - -
118B VAL* 3.5 18.9 + - - +
124B GLY* 5.2 0.7 - - - -
137B ILE* 3.6 31.9 - - + -
138B ALA* 4.8 7.6 - - - +
139B ALA* 4.2 11.6 - - + +
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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
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111B LEU* 2.7 26.6 + - - +
112B THR 3.7 3.1 - - - -
114B ALA* 1.3 76.4 - - - +
116B VAL* 1.3 60.5 + - - +
117B GLY 3.3 0.3 + - - -
118B VAL* 3.5 6.1 + - - +
124B GLY* 3.6 23.6 - - - -
158B ILE* 3.9 10.1 - - - +
160B VAL* 3.6 29.2 - - - +
173B ARG* 3.0 19.6 + - - -
177B LEU* 4.0 15.5 - - - -
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Residues in contact with VAL 116 (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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112B THR* 2.8 39.9 + - + +
113B ALA* 4.2 4.0 - - - +
115B SER* 1.3 72.0 - - - +
117B GLY* 1.3 60.6 + - - +
118B VAL 3.3 0.9 - - - +
173B ARG* 3.3 22.3 + - + +
174B PRO* 4.0 38.6 - - + -
177B LEU* 4.1 14.8 - - + -
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Residues in contact with GLY 117 (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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113B ALA 2.9 17.3 + - - -
114B ALA 4.0 2.9 - - - -
115B SER 3.2 0.4 - - - -
116B VAL* 1.3 77.5 - - - +
118B VAL* 1.3 62.5 + - - +
119B GLN* 3.2 13.0 + - - +
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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