Contacts of the helix formed by residues 155 - 167 (chain B) in PDB entry 6DU3
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 LEU 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B SER* 1.3 73.9 - - - +
156B ALA* 1.3 62.7 + - - +
157B LYS* 4.2 31.0 - - + +
158B TYR* 2.9 5.9 + - - +
159B ALA* 2.8 25.4 + - - -
178B ARG* 3.7 41.7 - - + +
179B GLU* 4.5 12.6 - - + +
859D ASP* 2.9 37.7 + - + +
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Residues in contact with ALA 156 (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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154B SER 3.9 1.4 + - - -
155B LEU* 1.3 72.8 - - - +
157B LYS* 1.3 63.4 + - - +
158B TYR 2.9 1.9 + - - -
160B ASP* 2.9 31.1 + - + +
161B PRO* 3.3 1.0 - - - +
177B PHE* 3.7 45.1 - - + +
179B GLU* 4.1 10.1 + - - +
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Residues in contact with LYS 157 (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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116B ILE* 4.0 4.2 - - - +
117B PRO 4.7 3.6 - - - +
118B VAL* 3.5 32.8 - - + +
119B GLU* 2.9 26.2 + - + +
120B ILE* 4.5 10.7 - - + +
121B ASP 5.5 0.4 - - - +
155B LEU* 4.2 28.1 - - + +
156B ALA* 1.3 77.1 - - - +
158B TYR* 1.3 58.2 + - + +
161B PRO* 3.6 16.7 - - - +
859D ASP* 5.6 2.2 - - + +
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Residues in contact with TYR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.1 9.6 - - + +
98B ASP* 2.7 35.4 + - - -
102B VAL* 4.2 6.6 - - - +
104B SER* 2.5 26.4 + - - -
116B ILE* 3.3 12.6 - - + +
118B VAL* 4.4 10.3 - - + -
127B VAL* 3.6 33.4 - - + -
129B VAL* 4.3 0.7 - - + -
154B SER* 3.7 18.2 - - - -
155B LEU 2.9 6.6 + - - +
157B LYS* 1.3 82.8 - - + +
159B ALA* 1.3 72.2 + - - +
160B ASP 3.3 1.3 - - - -
161B PRO* 3.2 9.4 - - - +
162B VAL* 3.2 39.5 - - + +
859D ASP 4.1 12.3 - - - +
860D LEU* 3.9 20.6 - - + -
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 3.8 16.6 - - + +
150B LEU* 4.7 2.5 - - + +
152B THR* 3.7 18.2 - - + -
154B SER* 3.2 24.9 - - - +
155B LEU 2.8 13.8 + - - +
158B TYR* 1.3 79.2 - - - +
160B ASP* 1.3 56.0 + - - +
162B VAL* 3.3 3.2 + - - +
163B ALA* 2.9 30.1 + - - +
177B PHE* 3.8 11.7 - - + -
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Residues in contact with ASP 160 (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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156B ALA* 2.9 24.8 + - + +
159B ALA* 1.3 77.2 - - - +
161B PRO* 1.3 64.2 - - + +
163B ALA* 3.4 1.0 + - - -
164B ASP* 3.0 24.8 + - - +
175B ARG* 2.9 36.8 + - - +
177B PHE* 3.2 29.1 - - + -
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Residues in contact with PRO 161 (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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116B ILE* 3.3 26.7 - - + -
117B PRO 5.9 0.4 - - - +
156B ALA 3.3 11.0 - - - +
157B LYS* 3.6 9.0 - - - +
158B TYR 3.2 13.7 - - - +
160B ASP* 1.3 88.4 - - + +
162B VAL* 1.3 65.0 + - - +
164B ASP* 3.2 13.2 + - + +
165B LEU* 3.0 30.5 + - + +
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Residues in contact with VAL 162 (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 LEU* 4.0 26.2 - - + -
102B VAL* 4.4 8.1 - - + -
114B PHE* 4.6 7.3 - - + -
116B ILE* 4.1 8.5 - - + -
129B VAL* 4.1 30.1 - - + -
158B TYR* 3.2 42.2 - - + +
159B ALA 3.3 8.0 + - - +
161B PRO* 1.3 77.0 - - - +
163B ALA* 1.3 52.3 + - - +
165B LEU* 3.1 9.3 + - - +
166B LEU* 2.7 39.7 + - + +
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Residues in contact with ALA 163 (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 LEU* 5.5 2.4 - - + +
150B LEU* 4.2 14.4 - - + -
159B ALA 2.9 16.9 + - - +
162B VAL* 1.3 76.4 - - - +
164B ASP* 1.3 64.5 + - - +
166B LEU* 4.3 7.4 - - - -
167B ASP* 2.9 29.7 + - - +
172B PHE* 4.7 10.5 - - + -
175B ARG* 3.4 36.0 + - - +
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Residues in contact with ASP 164 (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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160B ASP* 3.0 21.2 + - - +
161B PRO* 3.3 15.1 - - + +
163B ALA* 1.3 78.1 - - - +
165B LEU* 1.3 64.6 + - + +
167B ASP 4.3 8.1 + - - +
168B LYS* 5.3 1.2 - - - -
175B ARG* 3.0 26.7 + - - +
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Residues in contact with LEU 165 (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 PHE* 3.5 54.1 - - + -
115B ILE 5.1 7.2 - - - +
116B ILE* 5.5 5.8 - - + -
161B PRO* 3.0 25.2 + - + +
162B VAL* 3.8 5.4 - - - +
164B ASP* 1.3 80.8 - - + +
166B LEU* 1.3 65.5 + - - +
168B LYS* 4.6 9.0 + - - +
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Residues in contact with LEU 166 (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 LEU* 4.1 11.7 - - + -
101B LEU* 4.0 29.4 - - + -
102B VAL* 3.9 28.5 - - + -
114B PHE* 4.1 10.0 - - + -
131B LYS* 4.7 9.4 + - + +
135B VAL* 3.8 31.6 - - + -
136B ASP* 4.2 11.5 - - - +
139B LEU* 4.0 11.1 - - + +
162B VAL* 2.7 22.0 + - + +
163B ALA* 3.9 4.5 - - - +
165B LEU* 1.3 75.6 - - - +
167B ASP* 1.3 58.7 + - + +
168B LYS* 2.9 16.6 + - - +
169B TRP* 5.4 1.0 - - - -
172B PHE* 5.1 4.5 - - + -
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Residues in contact with ASP 167 (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 LEU* 4.7 6.4 - - + +
163B ALA 2.9 17.6 + - - +
164B ASP 4.7 5.5 - - - +
166B LEU* 1.3 72.5 - - - +
168B LYS* 1.3 61.4 + - - +
169B TRP* 3.0 14.0 + - - +
170B GLY* 3.0 15.2 + - - -
171B ALA* 2.8 30.2 + - - +
172B PHE* 2.8 55.7 + - + +
175B ARG* 5.2 5.5 + - - +
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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