Contacts of the helix formed by residues 124 - 137 (chain B) in PDB entry 6DC0
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 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B PHE 3.7 1.0 + - - -
123B PRO* 1.4 69.1 - - - +
125B LYS* 1.3 67.1 + - + +
126B HIS 3.1 1.7 + - - -
127B TYR* 3.3 35.3 + - + -
128B GLN* 4.6 3.3 + - - +
151B LEU* 3.9 22.4 - - + -
152B GLY 3.2 16.4 - - - +
153B GLU 3.8 8.3 - - - +
154B THR 3.0 19.0 + - - +
155B LYS 3.0 50.3 - - - +
156B ALA* 4.2 4.0 - - - +
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Residues in contact with LYS 125 (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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123B PRO* 3.0 4.7 + - + +
124B ILE* 1.3 83.0 - - + +
126B HIS* 1.3 81.6 + - + +
128B GLN* 5.2 2.3 + - - +
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Residues in contact with HIS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PHE* 4.9 2.5 - - - -
123B PRO* 2.9 22.3 + - + +
125B LYS* 1.3 95.2 - - + +
127B TYR* 1.3 65.9 + - - +
128B GLN 3.3 3.4 + - - +
129B ASP* 3.8 11.2 + - + +
130B LYS* 3.8 22.7 + - - +
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PHE* 4.0 22.4 - - + -
123B PRO 3.3 4.0 + - - +
124B ILE* 3.3 26.6 + - + +
126B HIS* 1.3 77.4 - - - +
128B GLN* 1.3 95.4 + - + +
130B LYS* 3.1 18.9 + - - +
131B ILE* 3.3 38.7 + - + +
149B VAL* 4.1 17.8 - - + +
151B LEU* 3.8 28.6 - - + +
156B ALA* 3.4 33.4 - - + -
158B VAL* 4.8 4.7 - - + -
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Residues in contact with GLN 128 (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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124B ILE 4.6 3.1 + - - +
125B LYS 5.2 2.0 + - - +
126B HIS* 3.3 2.0 - - - +
127B TYR* 1.3 117.6 + - + +
129B ASP* 1.3 67.8 + - - +
131B ILE* 3.4 6.7 + - - +
132B ARG* 3.3 23.0 + - - +
135B ILE* 5.4 0.2 - - - +
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Residues in contact with ASP 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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126B HIS* 3.8 7.6 + - - +
127B TYR 3.4 0.4 - - - -
128B GLN* 1.3 78.7 - - - +
130B LYS* 1.3 69.0 + - + +
132B ARG* 3.3 34.7 + - - +
133B PRO* 3.9 3.1 - - - +
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PHE* 3.6 39.2 - - + -
126B HIS* 3.8 20.2 + - - +
127B TYR 3.1 9.3 + - - +
129B ASP* 1.3 80.6 - - - +
131B ILE* 1.3 61.9 + - + +
133B PRO* 3.4 11.6 - - - +
134B TYR* 4.1 6.2 - - - -
227B GLU* 3.9 48.5 - - + +
228B ASP* 4.9 9.6 - - - -
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PHE* 5.0 2.0 - - + -
127B TYR* 3.3 36.3 + - + +
128B GLN* 3.7 9.9 - - - +
129B ASP 3.2 0.2 - - - -
130B LYS* 1.3 81.9 - - + +
132B ARG* 1.3 64.8 + - - +
133B PRO* 3.3 2.9 - - - -
134B TYR* 3.1 25.8 + - + +
135B ILE* 3.0 31.8 - - + +
146B ILE* 4.7 11.2 - - + -
149B VAL* 4.3 14.4 - - + -
158B VAL* 4.2 33.0 - - + -
160B PHE* 6.2 0.2 - - + -
227B GLU* 5.5 0.9 - - - +
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Residues in contact with ARG 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 GLN 3.3 19.9 + - - +
129B ASP* 3.3 27.8 + - - +
131B ILE* 1.3 76.0 - - - +
133B PRO* 1.3 68.4 - - + +
135B ILE* 3.2 11.3 + - + +
136B GLN* 2.8 57.2 + - - +
231B ILE* 3.9 29.9 - - + +
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Residues in contact with PRO 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 ASP 3.9 3.1 - - - +
130B LYS 3.4 13.0 - - - +
131B ILE 3.3 4.9 - - - -
132B ARG* 1.3 94.6 - - + +
134B TYR* 1.3 56.1 + - + +
136B GLN* 3.3 8.5 + - + +
137B LEU* 3.0 32.7 + - - +
201B ILE* 4.7 8.2 - - + +
226B LEU* 3.8 32.9 - - + +
227B GLU 5.2 2.7 - - - +
229B THR* 3.8 22.0 - - - +
231B ILE* 4.5 17.3 - - + -
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Residues in contact with TYR 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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130B LYS 4.1 11.4 - - - -
131B ILE* 3.1 21.7 + - + +
133B PRO* 1.3 76.2 - - + +
135B ILE* 1.3 60.2 + - + +
137B LEU* 3.0 24.8 - - - +
143B ILE* 5.8 0.2 - - + -
144B THR 3.2 27.8 - - - -
145B GLY* 4.4 2.5 - - - -
146B ILE* 3.6 43.1 - - + +
160B PHE* 3.3 17.3 - + - -
225B SER* 3.6 3.0 - - - -
226B LEU* 3.0 47.9 + - + -
227B GLU* 2.7 30.9 + - - -
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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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128B GLN 5.4 0.2 - - - +
131B ILE* 3.0 56.8 - - + +
132B ARG* 3.2 11.1 + - + +
133B PRO 3.2 0.2 - - - -
134B TYR* 1.3 81.3 - - + +
136B GLN* 1.3 75.3 + - - +
137B LEU 3.9 3.5 - - - +
146B ILE* 6.2 0.2 - - + -
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ARG* 2.8 65.9 + - - +
133B PRO* 3.3 6.7 + - + +
135B ILE* 1.3 96.5 - - - +
137B LEU* 1.3 61.1 + - - +
138B PRO* 3.6 7.3 - - - +
199B SER* 4.7 5.4 - - - +
201B ILE* 4.1 10.0 - - + +
231B ILE* 3.7 33.5 - - + +
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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 PRO 3.0 16.6 + - - +
134B TYR* 3.0 18.4 - - - +
135B ILE 3.9 2.9 - - - +
136B GLN* 1.3 77.4 - - - +
138B PRO* 1.4 89.1 - - + +
139B SER* 3.8 1.0 + - - -
143B ILE* 3.9 31.4 - - + -
195B HIS* 3.5 36.6 - - + +
196B CYS* 4.1 13.7 - - - -
199B SER* 3.6 19.5 - - - +
201B ILE* 4.8 10.1 - - + -
226B LEU* 4.3 11.0 - - + -
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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