Contacts of the helix formed by residues 103 - 118 (chain B) in PDB entry 1PN9
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 THR 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN* 3.2 23.1 + - - +
64A GLU* 4.7 3.6 + - - -
99B PHE* 2.8 45.2 + - + -
101B MET 3.4 0.8 - - - -
102B GLY* 1.3 78.2 + - - +
104B LEU* 1.3 65.8 + - - +
105B TYR 3.6 0.4 - - - -
106B GLN* 4.4 0.2 - - - -
107B ARG* 3.0 53.0 + - - +
133B ALA* 3.9 17.4 - - + +
136B PHE* 4.4 3.1 - - + -
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Residues in contact with LEU 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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99B PHE* 3.2 17.2 + - + -
100B ASP* 3.8 8.5 - - - +
103B THR* 1.3 81.3 - - - +
105B TYR* 1.3 63.5 + - - +
108B PHE 3.3 5.7 + - - -
133B ALA* 4.0 20.2 - - + +
134B VAL* 4.0 17.7 - - + +
137B LEU* 4.3 7.4 - - + -
159B LEU* 3.6 26.5 - - + -
162B THR* 3.6 22.9 - - + -
163B ILE* 3.7 23.8 - - + -
166B TYR* 2.6 44.8 + - + +
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Residues in contact with TYR 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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10B ALA* 3.8 22.2 + - + +
11B PRO* 4.3 13.7 - - + +
66B ARG* 4.3 11.0 - - - +
100B ASP 2.8 23.1 + - - +
101B MET* 4.3 6.7 - - + +
104B LEU* 1.3 72.9 - - - +
106B GLN* 1.3 61.6 + - - +
108B PHE* 3.0 24.2 + + - +
109B ALA* 2.9 33.9 + - + +
113B TYR* 2.3 35.4 + + - -
162B THR* 3.8 30.0 - - + +
165B THR* 5.3 3.4 - - + -
302B GTX 3.5 28.0 - - + +
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Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLY* 5.0 7.4 - - - +
106A GLN* 4.2 35.8 - - - +
110A ASP* 5.5 1.4 + - - -
101B MET* 3.1 23.3 + - - +
102B GLY* 3.3 23.1 - - - +
105B TYR* 1.3 82.4 - - - +
107B ARG* 1.3 58.9 + - + +
109B ALA* 3.4 6.6 + - - +
110B ASP* 2.8 66.0 + - - +
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Residues in contact with ARG 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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49A GLN* 5.7 1.6 - - - +
102B GLY 5.1 1.2 + - - +
103B THR* 3.0 37.7 + - - +
104B LEU 4.4 1.3 - - - +
106B GLN* 1.3 77.8 - - + +
108B PHE* 1.3 66.2 + - - +
110B ASP* 3.6 13.6 - - - +
111B TYR* 3.1 19.2 + - - +
126B ASN 4.6 1.2 - - - +
129B LYS* 3.1 50.8 + - + +
130B MET* 3.3 25.7 - - + +
132B ASP* 4.2 12.3 + - - +
133B ALA* 4.1 9.7 - - + +
136B PHE* 4.4 13.9 - - - -
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Residues in contact with PHE 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 LEU 3.3 13.2 + - - +
105B TYR* 3.0 29.6 + + - +
107B ARG* 1.3 81.5 - - - +
109B ALA* 1.3 62.1 + - - +
112B HIS* 2.9 65.4 + + + +
113B TYR* 4.9 4.7 - + - -
130B MET* 3.1 17.5 - - + +
165B THR* 3.5 29.4 - - + -
166B TYR* 3.5 50.1 + + + -
169B ALA* 3.9 2.0 - - + -
203B PHE* 4.4 10.5 - + - -
207B PHE* 4.0 14.4 - + - -
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Residues in contact with ALA 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 TYR* 2.9 23.7 + - + +
106B GLN* 3.7 9.6 - - - +
108B PHE* 1.3 75.1 - - - +
110B ASP* 1.3 64.6 + - - +
113B TYR* 2.8 76.6 + - + +
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Residues in contact with ASP 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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106A GLN* 5.9 0.7 + - - -
106B GLN* 2.8 55.0 + - - +
107B ARG* 3.6 14.2 - - + +
108B PHE 3.3 0.2 - - - -
109B ALA* 1.3 75.6 - - - +
111B TYR* 1.3 57.4 + - - +
114B PRO* 3.3 24.2 - - - +
126B ASN* 4.4 22.0 + - + +
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Residues in contact with TYR 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 ARG 3.1 7.6 + - - +
110B ASP* 1.3 80.0 - - - +
112B HIS* 1.3 79.8 + + - +
114B PRO* 4.1 3.8 - - - +
115B GLN* 2.9 41.5 + - - +
122B ALA* 3.5 21.3 - - + +
123B ASN* 3.3 33.2 + - - +
124B PRO* 5.0 0.4 - - + +
126B ASN* 3.9 13.4 - - + +
127B GLU* 3.3 44.4 + - + +
130B MET* 3.0 36.6 - - + -
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Residues in contact with HIS 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 PHE* 2.9 56.5 + + + +
111B TYR* 1.3 99.1 - + - +
113B TYR* 1.3 60.3 + - + +
114B PRO 3.3 2.0 - - - -
115B GLN* 3.0 12.7 + - - +
116B ILE* 2.7 46.2 + - + +
130B MET* 3.3 27.0 - - + +
169B ALA* 4.0 22.7 - - + +
207B PHE* 3.8 14.0 - + - -
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Residues in contact with TYR 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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105B TYR* 2.3 35.0 + + - -
108B PHE* 4.9 9.0 - + - -
109B ALA* 2.8 49.5 + - + +
112B HIS* 1.3 74.6 - - + +
114B PRO* 1.3 57.8 - - + +
116B ILE* 4.9 1.3 - - + -
117B PHE* 2.7 65.1 + + + +
203B PHE* 5.2 6.1 - + - -
302B GTX 2.8 31.0 + - + +
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Residues in contact with PRO 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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109B ALA 3.5 0.7 - - - +
110B ASP* 3.3 26.2 - - - +
111B TYR 4.1 3.6 - - - +
112B HIS 3.6 2.9 - - - -
113B TYR* 1.3 95.0 - - + +
115B GLN* 1.3 57.5 + - + +
118B ALA* 2.9 16.3 - - + +
119B LYS 2.8 22.0 + - - -
120B GLN* 2.9 31.5 + - + +
121B PRO 5.7 1.1 - - - +
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Residues in contact with GLN 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 TYR* 2.9 45.9 + - - +
112B HIS* 3.0 14.1 + - - +
114B PRO* 1.3 80.0 - - + +
116B ILE* 1.3 62.0 + - + +
119B LYS* 2.9 24.8 - - - +
120B GLN 3.2 23.5 + - - +
121B PRO 4.2 1.6 - - - +
122B ALA* 3.2 32.7 - - - +
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Residues in contact with ILE 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 HIS* 2.7 34.5 + - + +
113B TYR* 4.6 1.8 - - + +
115B GLN* 1.3 78.3 - - + +
117B PHE* 1.3 92.2 + - + +
119B LYS* 4.4 2.9 + - - +
203B PHE* 3.9 20.4 - - + -
206B LYS* 3.5 34.3 - - + +
207B PHE* 3.5 32.5 - - + -
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B MET* 4.1 35.2 - - + -
113B TYR* 2.7 57.0 + + + +
116B ILE* 1.3 99.7 - - + +
118B ALA* 1.3 57.3 + - + +
119B LYS 3.6 0.2 - - - -
203B PHE* 5.4 1.3 - + - -
206B LYS* 4.7 10.5 - - + -
302B GTX 4.4 26.9 - - + -
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Residues in contact with ALA 118 (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 TYR 3.7 0.2 + - - -
114B PRO* 2.9 20.8 + - + +
117B PHE* 1.3 77.3 - - + +
119B LYS* 1.3 60.1 + - - +
120B GLN* 2.7 40.4 + - + +
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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