Contacts of the helix formed by residues 128 - 146 (chain B) in PDB entry 4HI7
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 PRO 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B MET* 3.9 16.4 - - + -
126B GLU 4.7 0.4 - - - +
127B VAL* 1.3 91.0 - - + +
129B GLN* 1.3 66.5 + - - +
130B GLU* 3.0 23.8 - - + +
131B ARG* 2.9 35.6 + - + +
132B ILE 3.9 0.7 + - - -
219B VAL* 3.7 4.8 - - - +
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Residues in contact with GLN 129 (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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128B PRO* 1.3 73.2 - - - +
130B GLU* 1.3 63.5 + - - +
132B ILE* 3.0 23.5 + - - +
133B ASP* 2.9 54.6 + - - +
219B VAL* 3.5 31.2 - - + +
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Residues in contact with GLU 130 (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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124A LYS* 5.9 2.9 + - - -
128B PRO* 3.0 17.8 - - + +
129B GLN* 1.3 88.7 + - - +
131B ARG* 1.3 71.0 + - - +
133B ASP* 3.6 13.4 - - + +
134B ALA* 3.0 27.5 + - - +
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Residues in contact with ARG 131 (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 ASN* 3.0 31.9 + - - +
111B ALA 4.8 2.3 + - - +
114B SER* 3.3 28.8 + - - -
115B LEU* 4.0 26.1 - - + +
118B MET* 4.0 28.7 - - - -
127B VAL* 4.5 2.2 - - + -
128B PRO* 2.9 27.4 + - + +
130B GLU* 1.3 89.2 + - - +
132B ILE* 1.3 63.2 + - - +
134B ALA* 3.6 23.4 + - - +
135B ILE* 3.5 21.1 + - - +
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Residues in contact with ILE 132 (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 LEU* 4.2 18.8 - - + -
127B VAL* 4.9 2.7 - - + -
128B PRO 4.6 1.1 - - - +
129B GLN* 3.0 22.7 + - - +
131B ARG* 1.3 78.1 - - - +
133B ASP* 1.3 65.2 + - - +
135B ILE* 3.0 16.1 + - + +
136B THR* 3.1 19.9 + - + +
174B PHE* 5.2 2.5 - - + +
175B VAL* 4.3 25.6 - - + -
217B PHE* 4.5 18.6 - - + -
219B VAL* 3.9 28.3 - - + -
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Residues in contact with ASP 133 (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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129B GLN* 2.9 49.0 + - - +
130B GLU* 3.3 16.5 + - + +
132B ILE* 1.3 77.0 - - - +
134B ALA* 1.3 56.1 + - - +
136B THR* 3.3 9.1 + - - -
137B GLU* 2.9 48.7 + - + +
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Residues in contact with ALA 134 (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 VAL* 4.8 2.9 - - - +
110B ASN* 3.6 30.6 + - - +
111B ALA* 3.7 10.7 - - - +
130B GLU 3.0 17.1 + - - +
131B ARG* 3.7 21.5 - - - +
132B ILE 3.2 0.2 - - - -
133B ASP* 1.3 75.8 - - - +
135B ILE* 1.3 61.7 + - - +
137B GLU* 3.8 13.0 - - - +
138B ALA* 3.2 22.2 + - - +
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Residues in contact with ILE 135 (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* 4.1 11.9 - - + +
115B LEU* 3.8 18.6 - - + -
131B ARG 3.5 12.3 - - - +
132B ILE* 3.0 8.8 + - - +
134B ALA* 1.3 77.1 - - - +
136B THR* 1.3 67.2 + - - +
138B ALA* 3.1 6.4 + - - +
139B TYR* 3.0 54.3 + - + +
171B LEU* 3.7 28.3 - - + -
174B PHE* 3.7 29.4 - - + -
175B VAL* 3.9 17.5 - - + -
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Residues in contact with THR 136 (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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132B ILE* 3.1 17.4 + - + +
133B ASP* 3.3 14.9 + - - -
135B ILE* 1.3 76.5 - - + +
137B GLU* 1.3 59.4 + - - +
139B TYR* 3.3 6.9 + - + -
140B ASP* 2.8 38.7 + - - +
175B VAL* 4.3 22.9 - - + -
181B LYS* 5.1 6.3 - - - +
182B TYR* 3.6 14.9 + - + +
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Residues in contact with GLU 137 (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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117A LYS* 4.7 16.0 + - - -
106B VAL* 6.1 1.1 - - + -
110B ASN* 4.8 6.8 + - - -
133B ASP* 2.9 39.0 + - - +
134B ALA* 3.8 11.2 - - - +
136B THR* 1.3 76.8 + - - +
138B ALA* 1.3 61.4 + - - +
140B ASP* 3.3 10.5 + - - +
141B PHE* 2.9 43.9 + - + -
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Residues in contact with ALA 138 (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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102B PHE* 4.7 0.7 - - - -
106B VAL* 4.5 13.4 - - + +
107B VAL* 4.2 28.3 - - + -
111B ALA* 4.8 3.1 - - + -
134B ALA 3.2 11.6 + - - +
135B ILE* 3.1 11.1 + - - +
137B GLU* 1.3 78.5 - - - +
139B TYR* 1.3 68.0 + - + +
141B PHE* 3.2 11.2 + - - +
142B VAL* 3.0 29.5 + - + +
168B ILE* 6.4 1.1 - - + -
171B LEU* 4.9 2.7 - - + -
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Residues in contact with TYR 139 (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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135B ILE* 3.0 33.7 + - + +
136B THR* 3.3 9.6 + - + +
138B ALA* 1.3 79.6 - - + +
140B ASP* 1.3 63.0 + - - +
142B VAL* 3.3 2.4 + - - +
143B GLU* 3.0 26.3 + - - +
168B ILE* 4.3 15.7 - - + -
171B LEU* 3.5 36.6 + - + +
172B VAL* 3.6 5.4 + - - +
175B VAL* 2.7 39.2 + - + -
176B PRO 4.3 2.5 - - - -
177B VAL* 3.9 20.6 - - + -
182B TYR* 3.6 34.3 - + + -
185B LEU* 4.0 20.1 - - + +
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Residues in contact with ASP 140 (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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136B THR* 2.8 22.4 + - - +
137B GLU* 3.6 9.4 - - - +
139B TYR* 1.3 76.3 - - - +
141B PHE* 1.3 65.8 + - + +
143B GLU* 3.5 5.0 + - - +
144B ALA* 3.4 17.5 + - - +
181B LYS* 3.8 12.3 + - - -
182B TYR* 2.6 33.9 + - - -
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Residues in contact with PHE 141 (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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51A PRO 4.8 2.7 - - - -
52A GLN* 3.9 42.1 - - + +
53A HIS* 3.9 22.9 - + - -
113A ARG* 6.1 3.8 - - - -
102B PHE* 3.5 34.3 - + + -
106B VAL* 4.1 17.0 - - + -
137B GLU* 2.9 42.1 + - + -
138B ALA 3.2 1.5 + - - +
140B ASP* 1.3 79.9 - - + +
142B VAL* 1.3 62.1 + - - +
144B ALA* 3.2 15.3 + - + +
145B PHE* 3.4 20.9 + - + -
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Residues in contact with VAL 142 (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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102B PHE* 3.7 24.7 - - + -
107B VAL* 5.0 1.6 - - + -
138B ALA 3.0 18.1 + - - +
139B TYR* 4.0 3.6 - - - +
141B PHE* 1.3 72.1 - - - +
143B GLU* 1.3 66.9 + - - +
145B PHE* 2.9 34.4 + - + +
146B PHE* 3.3 19.2 - - + -
152B VAL* 4.6 7.2 - - + -
164B LEU* 4.4 5.4 - - + -
168B ILE* 4.0 22.2 - - + -
185B LEU* 3.8 25.6 - - + -
188B TRP* 5.0 0.9 - - + -
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Residues in contact with GLU 143 (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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139B TYR 3.0 17.9 + - - +
140B ASP* 3.7 6.3 - - - +
142B VAL* 1.3 76.6 - - - +
144B ALA* 1.3 60.7 + - - +
145B PHE 3.3 0.5 + - - -
146B PHE* 3.6 20.3 + - - +
147B LYS 4.8 0.3 + - - -
181B LYS 4.7 3.1 - - - +
182B TYR* 3.4 27.0 - - + -
183B PRO* 3.2 13.1 - - - +
184B LYS* 2.9 41.8 + - + +
185B LEU* 2.8 35.3 + - + +
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Residues in contact with ALA 144 (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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51A PRO* 4.7 23.3 - - + +
140B ASP 3.4 9.0 + - - +
141B PHE* 3.2 12.8 + - + +
142B VAL 3.1 1.0 - - - -
143B GLU* 1.3 77.9 - - - +
145B PHE* 1.3 66.6 + - + +
146B PHE 3.2 0.7 + - - -
147B LYS* 3.9 17.1 + - - +
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Residues in contact with PHE 145 (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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52A GLN* 3.8 20.4 - - + -
99B ARG* 3.4 60.4 + - - +
102B PHE* 3.7 48.7 - + - -
141B PHE 3.4 12.6 - - - -
142B VAL* 2.9 31.2 + - + +
144B ALA* 1.3 80.9 - - + +
146B PHE* 1.3 65.2 + - + +
147B LYS* 3.1 18.3 + - - +
149B GLN* 5.4 1.9 - - - +
151B TYR 4.8 2.0 - - - +
152B VAL* 4.2 20.0 - - + +
164B LEU* 4.3 5.2 - - + -
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Residues in contact with PHE 146 (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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142B VAL* 3.3 35.7 - - + -
143B GLU 3.6 8.5 - - - +
144B ALA 3.2 1.4 - - - -
145B PHE* 1.3 79.0 - - + +
147B LYS* 1.3 58.4 + - - +
149B GLN* 2.6 46.6 + - - +
150B THR 3.8 10.1 - - - -
151B TYR 3.7 24.5 - - - -
152B VAL* 4.0 13.5 - - + -
184B LYS* 3.7 33.4 - - + -
185B LEU* 3.8 20.2 - - - -
188B TRP* 3.4 49.4 - + + -
191B ARG* 5.5 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