Contacts of the helix formed by residues 108 - 122 (chain B) in PDB entry 1PRH
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 ILE 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B PHE* 5.7 5.2 - - + -
103B VAL* 3.9 24.5 - - + -
106B THR* 3.0 21.6 + - + +
107B PHE* 1.3 95.7 - - + +
109B ARG* 1.3 62.6 + - - +
111B THR* 3.0 12.5 + - + -
112B LEU* 2.8 50.5 + - + +
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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
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103B VAL 3.5 14.0 + - - +
104B ASN* 4.0 19.9 + - - +
106B THR 3.6 13.5 - - - +
107B PHE 3.1 0.2 - - - -
108B ILE* 1.3 75.8 - - - +
110B ASP* 1.3 55.2 + - - +
112B LEU* 3.7 1.9 - - - +
113B MET* 2.8 35.9 + - + +
346B GLU* 3.8 12.1 + - - -
357B LEU* 4.2 12.9 - - + +
358B GLN* 2.9 46.9 + - + +
359B LEU 2.9 23.6 + - - -
360B LYS* 3.3 36.4 - - + +
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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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106B THR 4.9 0.7 - - - +
107B PHE* 2.8 23.0 + - + +
109B ARG* 1.3 83.4 - - - +
111B THR* 1.3 55.7 + - - +
113B MET* 3.6 6.7 - - - +
114B ARG* 2.8 34.5 + - - +
360B LYS* 2.8 39.4 + - - +
362B ASP* 4.2 2.8 - - - +
365B LEU* 3.7 22.7 - - + +
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Residues in contact with THR 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* 3.1 24.0 + - - -
108B ILE* 3.0 15.7 + - + -
110B ASP* 1.3 76.5 - - - +
112B LEU* 1.3 71.1 + - + +
114B ARG* 3.1 22.9 + - - +
115B LEU* 2.9 33.2 + - + +
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Residues in contact with LEU 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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100B TRP* 3.5 36.1 - - + -
103B VAL* 3.8 10.3 - - + -
108B ILE* 2.8 32.6 + - + +
109B ARG 3.9 2.0 - - - +
111B THR* 1.3 76.6 - - + +
113B MET* 1.3 51.8 + - - +
115B LEU* 3.1 17.5 + - + +
116B VAL* 2.7 40.8 + - + +
357B LEU* 3.7 22.4 - - + -
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Residues in contact with MET 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 ARG* 2.8 20.6 + - + +
110B ASP* 3.6 7.4 - - - +
111B THR 3.2 0.2 - - - -
112B LEU* 1.3 76.3 - - - +
114B ARG* 1.3 61.1 + - - +
116B VAL* 3.2 15.9 + - + +
117B LEU* 3.1 56.0 + - + +
345B ILE* 4.5 12.6 - - + -
357B LEU* 4.8 3.3 - - + +
358B GLN 5.4 0.7 - - - +
359B LEU* 3.8 26.9 - - + -
360B LYS* 3.4 47.8 - - + +
365B LEU* 3.8 14.1 - - + -
531B LEU* 5.2 5.4 - - + -
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Residues in contact with ARG 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 ASP* 2.8 14.4 + - - +
111B THR* 3.4 29.1 + - - +
113B MET* 1.3 75.2 - - - +
115B LEU* 1.3 60.1 + - - +
117B LEU* 3.1 13.2 + - - +
118B THR* 2.9 37.4 + - + +
364B GLU 5.0 0.6 + - - -
365B LEU* 3.4 54.4 + - + +
366B LEU* 4.5 5.4 - - + -
369B ALA* 6.2 1.6 - - - -
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Residues in contact with LEU 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 THR* 2.9 25.2 + - + +
112B LEU* 3.3 16.8 - - + +
114B ARG* 1.3 81.2 - - - +
116B VAL* 1.3 67.8 + - + +
118B THR* 3.2 7.4 + - - -
119B VAL* 3.1 45.9 + - + +
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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 LEU* 2.7 28.0 + - + +
113B MET* 3.2 18.4 + - + +
115B LEU* 1.3 75.4 - - + +
117B LEU* 1.3 59.1 + - - +
119B VAL* 4.9 1.6 - - - -
120B ARG* 2.9 57.6 + - + +
355B TYR* 6.0 7.2 - - + -
357B LEU* 4.7 13.9 - - + -
359B LEU* 5.6 5.4 - - + -
531B LEU* 3.9 20.2 - - + -
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Residues in contact with LEU 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 MET* 3.1 40.4 + - + +
114B ARG* 3.1 9.6 - - - +
116B VAL* 1.3 77.9 - - - +
118B THR* 1.3 57.5 + - - +
121B SER* 2.8 38.4 + - - +
360B LYS 5.2 1.6 - - - +
362B ASP 5.1 1.6 - - - +
365B LEU* 4.0 28.9 - - + -
366B LEU* 4.0 22.7 - - + -
531B LEU* 4.1 19.7 - - + -
535B LEU* 3.5 37.0 - - + -
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Residues in contact with THR 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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114B ARG* 2.9 29.7 + - + +
115B LEU* 3.2 12.3 + - - +
117B LEU* 1.3 72.8 - - - +
119B VAL* 1.3 63.5 + - - +
121B SER* 3.6 2.4 - - - -
122B ASN* 2.9 44.8 + - - +
366B LEU* 3.9 19.7 - - + -
369B ALA* 3.9 18.8 - - + -
370B GLN 6.1 0.2 - - - +
371B PHE* 6.2 3.1 - - + -
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Residues in contact with VAL 119 (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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83B ARG* 5.4 9.6 - - - +
115B LEU* 3.1 35.4 + - + +
116B VAL* 4.1 1.8 - - - +
118B THR* 1.3 82.2 - - - +
120B ARG* 1.3 73.4 + - + +
122B ASN* 3.4 14.3 + - - +
123B LEU* 4.1 10.4 + - + +
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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
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89B ILE* 6.4 0.2 - - - +
116B VAL* 2.9 44.5 + - + +
119B VAL* 1.3 80.9 - - + +
121B SER* 1.3 63.2 + - - +
122B ASN 3.1 1.2 + - - -
123B LEU* 3.2 17.2 + - - +
355B TYR* 3.9 20.4 + - - -
523B ILE* 3.8 10.7 + - - +
524B GLU* 2.9 34.6 + - - +
527B ALA* 3.5 35.6 - - - +
528B PRO* 3.2 32.1 - - + +
531B LEU* 4.1 14.5 - - + +
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Residues in contact with SER 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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117B LEU* 2.8 25.9 + - - +
118B THR* 3.7 3.6 - - - -
120B ARG* 1.3 77.8 - - - +
122B ASN* 1.3 62.6 + - - +
123B LEU 3.1 1.0 + - - -
124B ILE* 3.2 20.3 + - - +
366B LEU* 5.6 0.5 - - - +
371B PHE* 3.6 34.9 - - - -
528B PRO* 4.9 8.5 - - - +
531B LEU* 4.3 6.1 + - - +
532B LYS* 4.2 25.0 + - - +
535B LEU* 5.6 0.9 - - - +
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Residues in contact with ASN 122 (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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118B THR* 2.9 33.0 + - - +
119B VAL* 3.9 9.3 - - - +
120B ARG 3.1 1.0 + - - -
121B SER* 1.3 79.2 - - - +
123B LEU* 1.3 63.4 + - + +
124B ILE 3.2 7.2 + - - +
370B GLN 4.6 13.3 + - - -
371B PHE* 5.8 3.0 - - - -
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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