Contacts of the helix formed by residues 152 - 163 (chain A) in PDB entry 2V5E
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 ASN 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLY* 1.3 75.7 - - - +
153A ASN* 1.3 65.6 + - - +
154A CYS* 2.9 9.0 + - - +
155A LEU* 2.6 53.5 + - - +
156A ASP* 3.1 27.2 + - - +
217A ARG* 5.0 10.8 - - - +
218A ASP* 4.7 7.3 + - - +
220A ALA* 4.3 8.3 + - - +
221A CYS* 3.7 41.7 - - + +
224A ARG* 4.3 2.9 - - - +
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Residues in contact with ASN 153 (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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152A ASN* 1.3 75.3 - - - +
154A CYS* 1.3 57.0 + - - +
156A ASP* 3.4 15.9 + - - +
157A ALA* 3.0 27.2 + - - +
214A CYS* 3.9 11.3 - - + +
215A SER* 3.0 41.5 + - - +
217A ARG* 3.7 26.1 + - - +
346A GLY 4.8 3.6 + - - -
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Residues in contact with CYS 154 (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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152A ASN* 2.9 7.9 + - - +
153A ASN* 1.3 74.1 - - - +
155A LEU* 1.3 65.4 + - - +
157A ALA* 3.2 4.6 + - - +
158A ALA* 3.0 22.0 + - - +
211A MET* 5.2 3.8 - - - +
214A CYS* 2.0 49.8 - - - -
216A CYS* 3.6 9.2 - - - -
221A CYS* 3.4 23.1 - - - +
224A ARG* 3.8 23.9 - - + -
225A ARG* 3.9 12.1 - - - +
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Residues in contact with LEU 155 (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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151A GLY* 4.3 10.3 - - - -
152A ASN* 2.6 45.2 + - - +
154A CYS* 1.3 71.4 - - - +
156A ASP* 1.3 60.5 + - - +
158A ALA* 3.1 6.0 + - - +
159A LYS* 2.8 29.4 + - - +
224A ARG* 3.3 38.6 - - - +
60B LYS* 3.8 44.4 - - + +
61B GLU* 4.5 4.7 - - + -
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Residues in contact with ASP 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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150A LYS 5.8 0.2 - - - +
152A ASN 3.1 18.5 + - - +
153A ASN* 3.6 19.8 - - - +
154A CYS 3.3 0.2 - - - -
155A LEU* 1.3 77.3 - - - +
157A ALA* 1.3 57.3 + - - +
159A LYS* 3.3 14.3 + - + +
160A ALA* 3.0 28.4 + - - +
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Residues in contact with ALA 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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153A ASN 3.0 15.8 + - - +
154A CYS 3.6 4.7 - - - +
155A LEU 3.2 0.2 - - - -
156A ASP* 1.3 73.0 - - - +
158A ALA* 1.3 61.0 + - - +
160A ALA* 3.4 6.8 + - - +
161A CYS* 2.9 30.0 + - - +
207A HIS* 5.2 2.4 - - - +
210A GLY* 3.3 41.5 - - - +
211A MET* 3.7 10.3 - - + +
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Residues in contact with ALA 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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154A CYS 3.0 9.3 + - - +
155A LEU* 3.4 8.7 - - - +
157A ALA* 1.3 74.1 - - - +
159A LYS* 1.3 63.1 + - - +
161A CYS* 3.4 1.6 + - - +
162A ASN* 3.0 30.0 + - - +
171A ARG* 4.0 1.3 - - - +
211A MET* 3.9 22.7 - - + +
224A ARG* 3.7 21.8 - - - +
61B GLU* 3.4 24.7 - - + +
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Residues in contact with LYS 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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155A LEU 2.8 16.4 + - - +
156A ASP* 3.4 17.0 - - + +
157A ALA 3.3 0.2 - - - -
158A ALA* 1.3 73.8 - - - +
160A ALA* 1.3 63.5 + - - +
162A ASN* 3.3 3.2 + - - -
163A LEU* 3.1 44.0 + - + +
47B HIS* 3.8 18.5 - - - -
61B GLU* 6.4 0.6 - - - +
62B GLU* 3.1 50.1 + - + +
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Residues in contact with ALA 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 ASP 3.0 16.1 + - - +
157A ALA* 3.8 7.4 - - - +
159A LYS* 1.3 76.9 - - - +
161A CYS* 1.3 62.5 + - - +
163A LEU* 3.3 8.3 + - - +
164A ASP* 3.2 22.3 + - - +
207A HIS* 4.1 20.9 + - + +
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Residues in contact with CYS 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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157A ALA 2.9 17.3 + - - +
158A ALA* 3.7 4.7 - - - +
160A ALA* 1.3 78.4 - - - +
162A ASN* 1.3 57.2 + - - +
163A LEU 3.1 0.2 - - - -
164A ASP 3.0 26.7 + - - +
167A CYS* 2.0 64.5 - - - +
168A LYS* 3.1 8.8 + - - -
171A ARG* 4.1 21.8 - - - -
207A HIS* 4.4 4.6 - - + -
211A MET* 3.9 13.5 - - + -
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Residues in contact with ASN 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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158A ALA 3.0 12.0 + - - +
159A LYS* 4.0 3.8 - - - +
161A CYS* 1.3 76.2 - - - +
163A LEU* 1.3 61.8 + - + +
164A ASP 3.4 1.3 - - - -
168A LYS* 3.5 32.6 + - - +
171A ARG* 3.0 33.2 + - - +
61B GLU* 3.2 12.3 + - - +
62B GLU 3.5 25.9 + - - +
64B ILE* 4.9 6.4 + - - +
111B LEU* 3.7 21.4 - - + +
112B SER 3.1 23.0 + - - +
113B PHE* 4.5 1.8 - - - +
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Residues in contact with LEU 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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159A LYS* 3.1 41.5 + - + +
160A ALA* 3.7 7.9 - - - +
161A CYS 3.1 0.2 - - - -
162A ASN* 1.3 81.9 - - + +
164A ASP* 1.3 59.0 + - - +
165A ASP* 4.2 2.0 + - - +
47B HIS* 4.0 26.2 - - + +
62B GLU 4.6 1.3 - - - -
63B LEU* 4.2 28.3 - - - +
64B ILE* 4.0 23.9 - - + +
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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