Contacts of the helix formed by residues 155 - 167 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A SER* 1.3 76.0 + - - +
156A ALA* 1.3 61.4 + - - +
157A LYS* 3.1 39.5 - - + +
158A TYR* 3.0 9.5 + - + +
159A ALA* 2.9 21.8 + - - +
177A PHE* 4.2 2.5 - - - -
178A ARG* 3.8 48.2 - - + +
179A GLU* 5.3 4.7 - - - +
860C LEU 4.7 0.2 + - - -
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 1.3 69.9 - - - +
157A LYS* 1.3 65.8 + - - +
159A ALA 3.6 0.7 - - - +
160A ASP* 3.0 43.1 + - - +
161A PRO* 3.5 0.9 - - - +
177A PHE* 3.6 40.0 - - + +
179A GLU* 5.6 2.6 + - - +
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Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 4.9 0.9 - - - +
117A PRO 5.1 1.4 - - - +
118A VAL* 4.0 24.9 - - + +
119A GLU* 3.1 33.7 + - + +
120A ILE* 4.8 6.6 - - + +
121A ASP 5.6 1.0 - - - +
155A LEU* 3.1 33.3 - - + +
156A ALA* 1.3 79.1 - - - +
158A TYR* 1.3 60.9 + - + +
161A PRO* 3.5 17.7 - - - +
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Residues in contact with TYR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.1 9.0 - - + +
98A ASP* 2.6 39.3 + - - -
102A VAL* 4.0 9.5 - - - +
104A SER* 2.7 24.9 + - - -
116A ILE* 4.4 2.8 - - + +
118A VAL* 4.2 26.7 - - + -
127A VAL* 4.0 21.5 - - + -
129A VAL* 4.7 1.1 - - + -
154A SER* 3.5 20.2 - - - -
155A LEU* 3.0 6.9 + - + +
156A ALA 3.0 0.2 - - - -
157A LYS* 1.3 81.4 - - + +
159A ALA* 1.3 66.2 + - - +
160A ASP 3.5 0.2 - - - -
161A PRO* 3.2 11.3 - - - +
162A VAL* 3.4 33.3 + - + +
860C LEU* 3.9 21.8 - - + -
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.4 12.9 - - + +
150A LEU* 4.7 3.1 - - + -
152A THR* 4.1 7.6 - - + -
154A SER* 3.6 16.6 - - - +
155A LEU 2.9 13.4 + - - +
158A TYR* 1.3 80.5 - - - +
160A ASP* 1.3 61.2 + - - +
162A VAL* 3.1 3.3 + - - +
163A ALA* 2.7 32.2 + - - +
177A PHE* 3.4 27.6 - - + -
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Residues in contact with ASP 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ALA* 3.0 23.5 + - - +
159A ALA* 1.3 77.1 - - - +
161A PRO* 1.3 60.8 - - + +
163A ALA* 4.4 0.4 - - - -
164A ASP* 2.8 39.2 + - - +
175A ARG* 2.6 42.4 + - - +
177A PHE* 3.5 18.2 - - - -
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Residues in contact with PRO 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 3.4 29.2 - - + -
156A ALA 3.5 1.6 - - - +
157A LYS 3.5 22.7 - - - +
158A TYR 3.2 10.5 - - - +
160A ASP* 1.3 94.7 - - + +
162A VAL* 1.3 62.5 + - - +
164A ASP* 3.3 11.0 + - + +
165A LEU* 3.1 26.0 + - + +
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.0 30.5 - - + -
102A VAL* 4.4 17.7 - - + -
114A PHE* 4.6 3.9 - - + -
116A ILE* 3.4 19.7 - - + -
129A VAL* 4.3 14.4 - - + -
158A TYR* 3.4 38.3 + - + +
159A ALA 3.1 7.5 + - - +
161A PRO* 1.3 75.0 - - - +
163A ALA* 1.3 59.7 - - - +
165A LEU* 3.0 8.4 + - - +
166A LEU* 2.9 30.0 + - + +
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 5.4 2.2 - - + +
150A LEU* 4.0 20.4 - - + -
159A ALA 2.7 19.7 + - - +
162A VAL* 1.3 74.0 - - - +
164A ASP* 1.3 63.6 + - - +
166A LEU* 4.4 7.4 - - - +
167A ASP* 2.9 30.1 + - - +
172A PHE* 4.3 11.4 - - + -
175A ARG* 3.3 30.1 - - - +
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Residues in contact with ASP 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ASP* 2.8 32.0 + - - +
161A PRO* 3.5 9.1 - - + +
162A VAL 3.2 0.2 - - - -
163A ALA* 1.3 73.0 - - - +
165A LEU* 1.3 64.8 + - + +
167A ASP 4.2 10.2 + - - +
168A LYS* 5.1 5.4 + - - +
175A ARG* 2.8 28.7 + - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 3.6 56.1 - - + -
115A ILE 5.6 1.3 - - - +
116A ILE* 4.7 10.8 - - + -
161A PRO 3.1 12.1 + - - +
162A VAL 3.0 8.3 + - - +
164A ASP* 1.3 78.5 - - + +
166A LEU* 1.3 64.3 + - - +
168A LYS* 3.5 32.6 - - - +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.2 16.4 - - + -
101A LEU* 4.2 12.6 - - + -
102A VAL* 3.7 25.8 - - + -
114A PHE* 4.2 6.3 - - + -
131A LYS* 4.0 37.2 - - + -
135A VAL* 4.1 14.6 - - + -
136A ASP* 4.1 8.3 - - - +
139A LEU* 4.1 20.1 - - + +
162A VAL* 2.9 20.9 + - + +
163A ALA* 4.0 4.9 - - - +
165A LEU* 1.3 76.3 - - - +
167A ASP* 1.3 60.6 + - + +
168A LYS* 2.8 14.0 + - - +
169A TRP* 3.5 13.9 - - - -
172A PHE* 5.0 4.0 - - + -
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Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.5 3.3 - - - +
163A ALA 2.9 16.2 + - - +
164A ASP 4.2 9.1 - - - +
165A LEU 3.6 0.2 - - - -
166A LEU* 1.3 72.9 - - - +
168A LYS* 1.3 60.4 + - - +
169A TRP* 3.4 7.5 + - - -
170A GLY* 2.9 17.6 + - - -
171A ALA* 2.6 32.7 + - - +
172A PHE* 2.7 53.7 + - + +
175A ARG* 5.1 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