Contacts of the helix formed by residues 144 - 156 (chain H) in PDB entry 5DST
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 SER 144 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78H ASP 5.0 1.2 - - - +
81H ALA* 3.2 22.7 + - - +
143H SER* 1.3 72.1 + - - +
145H ILE* 1.3 64.0 + - - +
146H SER* 3.0 3.1 - - - -
147H ASP* 3.1 31.0 + - - +
148H TYR* 4.1 8.1 + - - -
166H LYS* 3.9 17.9 - - - +
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Residues in contact with ILE 145 (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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250G ILE* 4.5 21.3 - - + -
80H TYR 3.6 13.7 - - - +
81H ALA* 3.9 19.7 - - - +
83H PHE* 4.7 7.2 - - + -
86H HIS* 3.5 30.7 - - + +
121H GLY* 3.9 10.3 - - - +
122H THR* 4.2 13.0 - - + +
141H GLU* 3.5 29.6 - - + -
143H SER* 3.8 9.6 + - - -
144H SER* 1.3 79.3 + - - +
146H SER* 1.3 58.8 + - - +
148H TYR* 2.9 31.8 + - + +
149H SER* 3.1 9.9 + - - -
401H SAH 4.4 0.4 - - - +
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Residues in contact with SER 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H GLU* 4.0 20.2 - - - -
143H SER 2.8 18.3 + - - -
144H SER 3.8 0.5 - - - -
145H ILE* 1.3 79.7 - - - +
147H ASP* 1.3 63.9 + - - +
149H SER* 2.7 26.6 + - - -
150H GLU* 3.0 17.5 + - - +
164H ILE* 4.2 10.1 - - - -
166H LYS* 2.9 33.5 - - - +
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Residues in contact with ASP 147 (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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144H SER* 3.1 20.8 + - - +
146H SER* 1.3 80.6 + - - +
148H TYR* 1.3 68.6 + - + +
150H GLU* 3.6 13.5 + - - +
151H LYS* 3.5 33.1 + - - +
166H LYS* 3.2 34.8 + - - +
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Residues in contact with TYR 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G CYS* 3.7 37.7 - - + -
250G ILE* 4.2 25.1 - - + -
253G VAL* 3.2 30.5 - - + +
81H ALA 5.5 4.3 - - - -
122H THR* 6.4 0.2 - - - -
144H SER* 4.2 11.2 - - - -
145H ILE* 2.9 23.7 + - + +
147H ASP* 1.3 79.1 - - + +
149H SER* 1.3 59.6 + - - +
151H LYS* 3.2 21.5 + - - +
152H ILE* 2.8 37.1 + - + +
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Residues in contact with SER 149 (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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120H SER* 3.9 4.4 + - - -
121H GLY 3.2 19.0 + - - -
122H THR* 3.1 29.0 + - - +
123H GLY* 4.0 5.8 - - - -
145H ILE 3.1 6.0 + - - -
146H SER* 2.7 27.1 + - - -
148H TYR* 1.3 75.0 - - - +
150H GLU* 1.3 55.2 + - - +
152H ILE* 3.3 1.8 + - - +
153H ILE* 2.8 42.1 + - - +
164H ILE* 3.8 14.0 - - - +
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Residues in contact with GLU 150 (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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146H SER 3.0 16.4 + - - +
147H ASP* 3.8 15.1 - - - +
148H TYR 3.2 0.4 - - - -
149H SER* 1.3 75.8 - - - +
151H LYS* 1.3 57.2 + - + +
153H ILE* 3.9 5.9 - - - +
154H LYS* 3.0 30.3 + - - +
159H ASP* 5.7 0.5 - - - +
164H ILE* 3.7 36.4 + - + +
166H LYS* 5.9 3.8 - - - +
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Residues in contact with LYS 151 (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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249G CYS* 4.2 25.8 - - + -
147H ASP* 3.5 19.6 + - - +
148H TYR* 3.2 27.7 + - + +
150H GLU* 1.3 75.5 - - + +
152H ILE* 1.3 60.9 + - - +
154H LYS* 3.6 6.3 + - - +
155H ALA* 2.9 29.7 + - - +
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Residues in contact with ILE 152 (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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246G ASP 3.6 15.5 - - - +
247G MET* 4.0 25.8 - - + -
249G CYS* 3.6 15.9 - - - -
250G ILE* 3.9 28.5 - - + -
122H THR* 3.8 19.5 - - + +
127H MET* 3.8 22.7 - - + -
148H TYR* 2.8 28.7 + - + +
149H SER 3.5 3.8 - - - +
151H LYS* 1.3 74.7 - - - +
153H ILE* 1.3 61.6 + - + +
155H ALA* 3.1 6.5 + - - +
156H ASN* 2.4 38.8 + - - +
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Residues in contact with ILE 153 (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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123H GLY* 4.9 9.2 - - - +
127H MET* 4.0 27.6 - - + -
149H SER* 2.8 28.3 + - - +
150H GLU* 3.9 5.2 - - - +
152H ILE* 1.3 74.2 - - + +
154H LYS* 1.3 66.4 + - - +
156H ASN* 3.0 11.4 + - - +
157H HIS 3.3 8.0 + - - -
158H LEU* 3.3 35.4 + - + +
159H ASP* 3.6 10.8 - - + +
162H ILE* 3.6 33.9 - - + +
164H ILE* 3.8 23.6 - - + -
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Residues in contact with LYS 154 (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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150H GLU 3.0 18.4 + - - +
151H LYS* 3.8 6.1 - - - +
153H ILE* 1.3 78.5 - - - +
155H ALA* 1.3 61.4 + - - +
157H HIS* 3.1 20.3 + - - -
159H ASP* 3.4 36.1 - - + +
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Residues in contact with ALA 155 (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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246G ASP* 4.3 21.8 - - - +
151H LYS 2.9 18.9 + - - +
152H ILE* 3.1 9.8 + - - +
154H LYS* 1.3 76.8 - - - +
156H ASN* 1.3 62.0 + - - +
157H HIS* 3.4 15.3 + - - -
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Residues in contact with ASN 156 (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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244G GLY 4.6 1.2 - - - +
245G PHE* 3.5 24.9 - - + +
246G ASP* 2.9 46.2 + - - +
127H MET* 4.0 8.3 - - - -
131H LYS* 5.3 4.7 + - - -
152H ILE* 2.4 35.1 + - - +
153H ILE 3.0 5.1 + - - +
155H ALA* 1.3 77.3 - - - +
157H HIS* 1.3 76.0 + - - +
158H LEU* 3.3 14.1 + - + +
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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