Contacts of the helix formed by residues 105 - 119 (chain B) in PDB entry 4HRE
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 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B ASN* 3.7 5.2 - - - +
69B GLN* 3.8 25.7 - - + +
104B LYS* 1.3 73.5 - - - +
106B PRO* 1.3 65.5 - - - +
107B ALA* 3.8 6.5 + - - +
108B GLN* 2.9 32.9 + - - +
109B TYR* 2.8 31.2 + - - +
146B VAL* 5.4 1.4 - - - +
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Residues in contact with PRO 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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65B ASN* 3.7 24.7 - - + +
105B THR* 1.3 85.4 - - - +
107B ALA* 1.3 63.5 + - - +
109B TYR* 3.9 4.4 - - + +
110B ASP* 3.0 35.5 + - - +
139B GLU* 5.6 5.2 - - - +
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Residues in contact with ALA 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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105B THR* 3.2 6.1 + - - +
106B PRO* 1.3 79.6 - - - +
108B GLN* 1.3 58.2 - - - +
110B ASP* 4.1 1.0 - - - +
111B ALA* 3.0 32.1 + - - +
139B GLU 5.6 0.4 - - - -
142B GLU* 4.0 24.7 - - + +
143B ILE* 4.3 11.8 - - - +
145B ARG* 4.8 3.8 - - - +
146B VAL* 3.6 28.7 - - + +
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Residues in contact with GLN 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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69B GLN* 5.4 1.7 - - - +
103B LEU 5.1 1.3 + - - +
104B LYS* 3.4 31.7 - - + +
105B THR* 2.9 37.5 + - - +
107B ALA* 1.3 77.6 - - - +
109B TYR* 1.3 57.4 + - - +
111B ALA* 3.7 1.6 - - - +
112B SER* 2.9 32.3 + - - -
146B VAL* 4.1 13.7 - - + +
150B MET* 4.0 21.0 - - + +
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Residues in contact with TYR 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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97B THR* 5.3 4.4 + - + +
101B GLY* 3.7 30.4 - - - +
104B LYS* 3.9 22.6 - - + +
105B THR 2.8 15.9 + - - +
106B PRO* 3.9 5.2 - - + +
108B GLN* 1.3 74.9 - - - +
110B ASP* 1.3 75.6 + - - +
112B SER* 3.1 7.4 + - - -
113B GLU* 3.0 51.6 + - + +
289B ILE* 4.1 11.3 - - - +
290B ARG* 3.4 46.6 + - + +
293B VAL* 3.8 24.6 - - + +
294B SER* 4.7 6.7 - - - -
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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 PRO* 3.0 21.1 + - - +
109B TYR* 1.3 87.1 - - - +
111B ALA* 1.3 63.6 + - - +
113B GLU* 3.3 1.2 + - - -
114B LEU* 3.0 29.9 + - - +
131B ILE* 3.6 15.6 - - + +
135B ARG* 2.8 44.8 + - - +
139B GLU* 5.2 3.5 - - - +
143B ILE* 3.6 28.5 - - + +
294B SER* 4.5 2.6 - - - -
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Residues in contact with ALA 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 ALA 3.0 20.3 + - - +
108B GLN 3.7 4.7 - - - +
110B ASP* 1.3 77.1 - - - +
112B SER* 1.3 62.8 + - - +
114B LEU* 3.2 15.4 + - - +
115B LYS* 3.1 17.0 + - - +
143B ILE* 4.3 6.7 - - + +
146B VAL 4.5 0.7 - - - -
147B TYR* 3.7 40.8 - - + +
150B MET* 4.3 11.0 - - - -
151B TYR* 4.3 1.6 - - + -
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Residues in contact with SER 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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104B LYS* 3.9 23.0 + - - +
108B GLN 2.9 16.7 + - - -
109B TYR* 3.1 18.5 + - - -
111B ALA* 1.3 76.5 - - - +
113B GLU* 1.3 57.8 + - - +
115B LYS* 3.3 2.9 + - - +
116B ALA* 3.1 27.4 + - - +
150B MET* 4.0 7.2 - - - +
151B TYR* 3.3 23.0 + - - -
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Residues in contact with GLU 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 TYR* 3.0 54.7 + - + +
110B ASP 3.6 4.3 - - - +
112B SER* 1.3 75.9 + - - +
114B LEU* 1.3 61.8 + - - +
116B ALA* 3.4 8.9 + - - +
117B SER* 2.9 28.6 + - - -
127B SER* 5.1 4.6 + - - -
131B ILE* 3.7 16.8 - - + -
286B LYS* 5.2 5.9 - - - +
290B ARG* 3.1 35.1 + - + +
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Residues in contact with LEU 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 3.0 22.0 + - - +
111B ALA* 3.2 8.5 + - - +
113B GLU* 1.3 77.2 - - - +
115B LYS* 1.3 53.1 + - - +
117B SER* 2.6 18.5 + - - -
118B MET* 2.7 33.6 + - + +
127B SER 5.5 0.4 - - - -
128B LEU* 3.5 35.0 - - + -
131B ILE* 3.9 32.8 - - + -
132B ILE* 4.3 10.8 - - + -
143B ILE* 3.7 28.3 - - + -
147B TYR* 4.2 4.5 - - + -
155B LEU* 4.2 15.7 - - + -
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Residues in contact with LYS 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 ALA 3.1 6.6 + - - +
112B SER 3.3 4.7 + - - +
114B LEU* 1.3 73.5 - - - +
116B ALA* 1.3 61.2 + - - +
118B MET* 3.4 11.3 + - + +
119B LYS* 2.9 71.0 + - - +
147B TYR* 3.4 19.9 - - + +
151B TYR* 3.5 55.0 - - + +
158B ASP* 4.2 17.8 + - - +
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Residues in contact with ALA 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 SER 3.1 16.1 + - - +
113B GLU* 3.8 11.4 - - - +
115B LYS* 1.3 75.8 - - - +
117B SER* 1.3 66.4 + - - +
119B LYS* 3.4 19.7 + - - +
124B ASP* 5.5 0.3 - - - +
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Residues in contact with SER 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 GLU 2.9 15.0 + - - -
114B LEU* 2.6 25.9 + - - -
116B ALA* 1.3 79.0 - - - +
118B MET* 1.3 64.8 + - - +
119B LYS 3.4 2.9 + - - +
123B THR* 3.0 18.9 - - - +
124B ASP* 3.1 39.0 + - - +
127B SER* 4.1 16.2 - - - -
128B LEU* 4.0 17.2 - - - +
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Residues in contact with MET 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 LEU* 2.7 33.1 + - + +
115B LYS* 3.6 16.4 - - - +
117B SER* 1.3 75.3 + - - +
119B LYS* 1.3 57.1 + - - +
120B GLY 2.8 10.0 + - - +
123B THR* 3.9 0.7 - - - -
128B LEU* 4.5 22.2 - - + -
147B TYR* 3.7 16.8 - - - +
155B LEU* 3.9 23.8 - - + -
158B ASP* 3.6 41.7 - - + +
159B ILE* 4.3 6.5 - - + -
162B ASP* 2.7 44.9 - - - +
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Residues in contact with LYS 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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115B LYS* 2.9 49.7 + - - +
116B ALA* 3.7 13.1 - - - +
117B SER 3.3 8.7 - - - +
118B MET* 1.3 78.0 - - - +
120B GLY* 1.3 61.8 + - - +
122B GLY 3.7 5.5 - - - +
124B ASP 5.3 0.2 + - - -
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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