Contacts of the helix formed by residues 128 - 145 (chain B) in PDB entry 6DWN
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 GLY 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LYS* 5.2 4.9 - - - -
126B ASP* 3.2 8.9 + - - -
127B SER* 1.3 82.0 + - - +
129B PRO* 1.3 77.1 - - - +
130B VAL 3.2 2.2 - - - -
131B TRP* 3.2 11.4 + - - +
132B ALA* 3.3 10.1 + - - +
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Residues in contact with PRO 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ASP* 5.6 12.1 - - + +
128B GLY* 1.3 83.9 - - - +
130B VAL* 1.3 73.0 + - + +
132B ALA* 3.3 8.2 + - + +
133B ALA* 3.0 24.5 + - - +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 3.3 23.3 - - - +
128B GLY 3.2 0.8 - - - -
129B PRO* 1.3 84.3 - - + +
131B TRP* 1.3 63.6 + - - +
133B ALA* 3.4 6.5 + - - +
134B ARG* 3.1 41.5 + - + +
303B SER 5.8 4.5 - - - +
306B LYS* 4.6 17.7 - - + +
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Residues in contact with TRP 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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104B LYS* 4.6 16.2 - - + -
121B MET* 3.6 27.7 + - + +
126B ASP* 3.6 27.6 + - + +
127B SER* 3.8 22.0 - - - -
128B GLY 3.2 8.5 + - - +
130B VAL* 1.3 78.9 - - - +
132B ALA* 1.3 81.6 + - + +
134B ARG* 3.0 12.3 + - - +
135B ARG* 2.8 49.8 + - - +
454B LYS* 3.3 37.7 - - + -
455B ARG* 3.0 47.2 - - + +
601B HEM 3.2 9.0 + - - -
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Residues in contact with ALA 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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128B GLY 3.3 6.4 + - - +
129B PRO* 3.8 10.5 - - + +
131B TRP* 1.3 102.0 - - + +
133B ALA* 1.3 62.1 + - - +
135B ARG* 3.4 7.0 + - - +
136B ARG* 3.2 47.5 + - - +
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Residues in contact with ALA 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 PRO 3.0 17.0 + - - +
130B VAL* 3.6 8.1 - - - +
131B TRP 3.1 0.2 - - - -
132B ALA* 1.3 76.4 - - - +
134B ARG* 1.3 63.8 + - + +
136B ARG* 3.3 15.0 + - - +
137B LEU* 3.2 25.7 + - + +
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Residues in contact with ARG 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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119B GLN 2.9 29.1 + - - -
120B SER 4.5 1.2 - - - -
121B MET* 3.4 42.2 - - + +
124B SER* 4.6 5.7 + - - -
126B ASP* 4.4 10.9 + - - +
130B VAL* 3.1 29.3 + - + +
131B TRP* 3.0 10.1 + - - +
133B ALA* 1.3 76.0 - - + +
135B ARG* 1.3 64.0 + - - +
137B LEU* 3.1 12.3 + - + +
138B ALA 3.0 17.5 + - - -
306B LYS* 3.0 54.7 + - + +
307B ILE* 5.5 4.0 - - + -
309B ASN* 3.2 9.7 + - - -
310B ILE* 3.6 22.8 - - + +
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Residues in contact with ARG 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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121B MET* 3.8 11.6 - - - -
131B TRP* 2.8 43.6 + - - +
132B ALA* 3.6 8.3 - - - +
134B ARG* 1.3 73.2 - - - +
136B ARG* 1.3 57.8 + - + +
138B ALA* 3.0 5.9 + - - +
139B GLN* 2.8 44.9 + - - +
454B LYS 3.3 18.7 + - - -
455B ARG* 3.9 1.4 - - - +
456B LYS* 2.6 44.5 + - - +
458B ILE* 3.3 26.3 - - + +
601B HEM 2.5 46.3 + - + +
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ALA* 3.2 40.7 + - - +
133B ALA* 3.7 13.5 - - - +
135B ARG* 1.3 78.2 - - + +
137B LEU* 1.3 58.0 + - - +
139B GLN* 3.2 17.6 + - - +
140B ASN* 2.8 47.4 + - - +
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Residues in contact with LEU 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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133B ALA* 3.2 13.8 + - + +
134B ARG* 3.1 12.0 + - + +
136B ARG* 1.3 79.2 - - + +
138B ALA* 1.3 56.6 + - - +
140B ASN* 4.1 8.0 - - + +
141B GLY* 2.8 28.1 + - - -
281B ILE* 5.7 0.9 - - - +
284B SER* 5.4 2.1 + - - +
285B LEU* 4.3 16.1 - - + +
288B HIS* 3.6 50.7 - - + +
307B ILE* 4.2 24.0 - - + -
310B ILE* 4.3 15.5 - - + -
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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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121B MET* 4.2 5.2 - - + -
134B ARG 3.0 8.6 + - - +
135B ARG 3.0 8.1 + - - +
137B LEU* 1.3 73.1 - - - +
139B GLN* 1.3 60.0 + - - +
141B GLY* 5.0 0.4 - - - -
142B LEU* 2.8 35.5 + - - +
281B ILE* 6.1 1.1 - - - -
285B LEU* 6.2 0.2 - - - -
310B ILE* 3.8 26.4 - - + +
314B LEU* 3.9 13.1 - - + +
458B ILE* 3.4 25.6 - - + -
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Residues in contact with GLN 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 ARG* 2.8 42.0 + - - +
136B ARG* 3.6 28.0 + - - +
138B ALA* 1.3 73.5 - - - +
140B ASN* 1.3 62.0 + - - +
142B LEU* 3.7 5.4 - - - +
143B LYS* 2.9 36.0 + - - +
456B LYS* 6.0 3.4 - - - +
458B ILE* 4.3 24.7 - - + +
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Residues in contact with ASN 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 ARG* 2.8 36.0 + - - +
137B LEU* 4.1 8.0 - - + +
139B GLN* 1.3 75.0 - - - +
141B GLY* 1.3 58.4 + - - +
143B LYS* 4.4 18.8 + - - +
144B SER* 2.8 40.7 + - - +
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Residues in contact with GLY 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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137B LEU 2.8 22.4 + - - -
138B ALA 3.7 0.9 - - - -
140B ASN* 1.3 73.2 - - - +
142B LEU* 1.3 61.5 + - - +
144B SER* 4.6 0.9 - - - -
145B PHE* 3.2 29.5 + - - -
281B ILE* 3.3 23.8 - - - +
284B SER* 4.3 15.0 - - - -
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Residues in contact with LEU 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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138B ALA 2.8 23.1 + - - +
139B GLN* 3.7 3.8 - - - +
141B GLY* 1.3 70.1 - - - +
143B LYS* 1.3 62.7 + - - +
145B PHE 3.1 1.9 + - - -
146B SER* 2.3 35.4 + - - -
198B ILE* 5.0 2.5 - - + -
201B ILE* 4.5 9.0 - - + -
281B ILE* 3.8 19.2 - - + +
314B LEU* 3.9 15.3 - - + -
458B ILE* 3.6 44.0 - - + +
462B ILE* 3.6 26.5 - - + -
601B HEM 4.1 23.3 - - + -
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Residues in contact with LYS 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 GLN* 2.9 24.9 + - - +
140B ASN* 3.8 18.0 + - - +
142B LEU* 1.3 74.8 - - - +
144B SER* 1.3 63.5 + - - +
145B PHE 3.3 0.7 + - - -
146B SER* 3.8 4.0 - - - -
147B ILE* 3.4 25.2 + - + +
148B ALA* 3.2 22.7 + - - +
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Residues in contact with SER 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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140B ASN* 2.8 29.3 + - - +
141B GLY* 4.6 0.2 - - - -
142B LEU 3.2 0.4 - - - -
143B LYS* 1.3 75.8 - - - +
145B PHE* 1.3 84.3 + - - +
146B SER 3.7 0.2 - - - -
148B ALA* 3.4 20.8 - - - +
158B TYR* 4.0 7.6 - - - -
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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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141B GLY* 3.2 22.4 - - - +
142B LEU 3.1 4.1 + - - -
144B SER* 1.3 95.0 - - - +
146B SER* 1.3 60.3 + - - +
158B TYR* 3.6 37.5 - + + +
162B HIS* 5.1 0.5 + - - -
201B ILE* 3.6 26.3 - - + +
278B ILE* 3.3 36.3 - - + -
279B ARG 3.6 10.5 - - - -
280B ASP* 3.4 38.4 - - - -
281B ILE* 4.0 16.2 - - + -
284B SER* 3.9 16.8 - - - -
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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