Contacts of the helix formed by residues 154 - 159 (chain H) in PDB entry 1PV2
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 154 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H GLY 3.4 10.3 - - - -
74H HIS* 3.9 5.4 - - - -
77H GLU* 3.4 7.7 + - - -
105H GLU* 3.8 13.9 - - - -
153H GLY* 1.3 73.5 - - - -
155H HIS* 1.3 61.4 + - - -
156H GLY 2.9 12.6 + - - -
157H ALA* 2.9 19.1 + - - +
185H CYS* 3.8 12.8 - - - -
186H HIS* 3.8 7.0 - - - +
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Residues in contact with HIS 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H LEU* 4.1 7.0 - - + +
69H PHE* 3.7 25.3 - + + -
71H THR* 3.3 22.1 + - + +
105H GLU* 4.0 4.9 + - - -
154H GLY* 1.3 72.9 - - - -
156H GLY* 1.3 61.5 + - - +
157H ALA 3.1 0.4 - - - -
158H LEU* 3.2 34.7 + - + +
159H ILE* 4.2 5.4 + - - +
185H CYS* 5.9 1.3 - - - -
186H HIS* 3.1 38.8 + + - -
209H PHE* 5.5 2.6 - - - -
214H ASP* 3.1 20.4 + - - -
217H THR* 6.1 0.2 - - - +
222H TYR* 4.1 22.6 - + - -
223H MET* 4.1 16.9 - - - -
227H LEU* 4.4 4.7 - - + +
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Residues in contact with GLY 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H ALA* 3.5 20.5 - - - +
58H GLU 4.4 0.2 - - - -
71H THR* 3.3 2.4 + - - -
72H GLY* 3.1 31.2 + - - -
154H GLY 2.9 2.8 + - - -
155H HIS* 1.3 80.1 - - - +
157H ALA* 1.3 60.5 + - - +
159H ILE* 3.1 33.3 + - - +
161H LEU* 5.2 0.2 - - - +
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Residues in contact with ALA 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H ALA* 4.4 3.7 - - - +
72H GLY 4.7 0.2 + - - -
73H ASN* 4.8 3.6 - - - +
152H PRO 4.0 19.5 - - - +
153H GLY 4.6 0.4 - - - +
154H GLY 2.9 15.2 + - - +
156H GLY* 1.3 77.4 - - - +
158H LEU* 1.3 61.3 + - - +
159H ILE 3.2 0.9 + - - -
161H LEU* 3.5 34.3 - - + +
162H PRO* 3.6 8.5 - - - +
186H HIS* 3.8 22.9 - - + +
187H GLY* 4.1 4.9 - - - +
189H ALA* 4.8 2.4 - - - +
190H ALA 5.2 0.5 + - - -
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Residues in contact with LEU 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H LEU* 4.2 22.7 - - + +
155H HIS* 3.5 26.9 - - - +
156H GLY 3.1 0.8 - - - -
157H ALA* 1.3 78.3 - - - +
159H ILE* 1.3 59.9 + - - +
160H GLY 3.5 1.4 + - - -
162H PRO* 3.3 20.6 - - - +
163H GLU* 6.0 0.2 - - - +
186H HIS* 3.6 40.2 - - + +
189H ALA* 3.6 26.0 - - + -
227H LEU* 4.4 13.0 - - + -
229H TRP* 4.1 24.4 + - + +
231H PHE* 4.3 11.0 - - + -
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Residues in contact with ILE 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G LEU* 4.8 9.2 - - + -
56H ALA* 5.5 1.4 - - - +
57H ASP* 4.9 6.6 - - - +
58H GLU* 3.6 49.1 - - + +
59H ARG 4.3 1.6 - - - -
60H TYR 3.5 29.4 - - - +
61H LEU* 3.9 24.2 - - + +
62H PRO* 5.5 2.2 - - + -
71H THR* 4.6 0.7 - - + -
155H HIS 4.2 0.7 - - - +
156H GLY* 3.1 24.0 + - - +
158H LEU* 1.3 76.9 - - - +
160H GLY* 1.3 62.3 + - - +
161H LEU* 3.0 17.3 + - - +
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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