Contacts of the helix formed by residues 149 - 160 (chain G) in PDB entry 2HPC
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 ARG 149 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145G VAL* 3.5 29.2 + - - +
146G ASP* 4.0 5.2 - - - +
148G LYS* 1.3 81.3 - - - +
150G LEU* 1.3 59.9 + - - +
151G GLU 3.0 1.1 - - - -
152G VAL 3.7 1.7 - - - +
153G ASP* 2.8 31.9 + - - +
424H TRP* 3.1 56.9 + - - -
425H ASP* 3.8 5.9 - - - +
426H MET* 3.0 33.7 - - - +
427H ALA 3.3 18.2 + - - +
428H LYS* 5.0 8.1 + - - -
429H HIS* 5.4 1.8 - - - +
430H GLY* 4.6 8.2 - - - +
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Residues in contact with LEU 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G ASP* 2.8 20.6 + - - +
147G MET* 3.6 36.8 - - + -
149G ARG* 1.3 73.2 - - - +
151G GLU* 1.3 71.3 + - - +
153G ASP* 3.7 10.7 - - + +
154G ILE* 3.2 46.7 + - + +
182H LEU* 5.9 1.6 - - + +
121I ILE* 3.7 19.3 - - + -
124I LEU* 4.2 20.6 - - + +
125I LYS* 3.5 24.2 - - + +
128I VAL* 5.5 3.8 - - + -
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Residues in contact with GLU 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G MET 3.2 23.4 + - - +
148G LYS* 4.2 6.1 - - - -
150G LEU* 1.3 86.5 - - - +
152G VAL* 1.3 65.2 + - + +
153G ASP 2.9 0.5 + - - -
154G ILE* 2.8 19.6 + - - +
155G ASP* 3.0 15.2 + - - +
171G ARG* 4.2 0.7 + - - -
173G VAL* 2.6 48.5 - - + +
174G ASP 5.2 0.2 + - - -
175G LEU* 5.0 2.9 - - + -
178G TYR* 4.0 17.3 - - + -
178H LYS* 5.6 0.2 - - - +
182H LEU* 3.1 42.2 - - + +
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Residues in contact with VAL 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G LYS 3.1 23.6 - - - +
149G ARG 3.5 0.6 + - - -
151G GLU* 1.3 82.6 - - + +
153G ASP* 1.3 60.2 + - - +
155G ASP* 3.8 17.9 - - - +
156G ILE* 3.2 23.6 + - + +
173G VAL* 5.6 1.6 - - + -
175G LEU* 4.9 9.0 - - + -
417H TYR* 4.0 29.4 - - + +
426H MET* 3.9 41.7 - - + +
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Residues in contact with ASP 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G ARG 2.8 23.3 + - - +
150G LEU* 3.7 12.9 - - + +
151G GLU 2.9 0.2 + - - -
152G VAL* 1.3 70.9 - - - +
154G ILE* 1.3 64.1 + - - +
156G ILE* 3.3 5.3 - - - +
157G LYS* 2.9 64.0 + - - +
415H ARG* 2.8 31.3 + - - +
426H MET 5.0 0.4 + - - -
428H LYS* 4.3 17.7 - - + +
128I VAL* 4.6 6.1 - - - +
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Residues in contact with ILE 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G LEU* 3.2 36.1 - - + +
151G GLU 2.8 7.6 + - - +
153G ASP* 1.3 74.3 - - - +
155G ASP* 1.3 56.7 + - - +
156G ILE 3.0 1.6 - - - -
157G LYS* 3.0 6.6 + - - +
158G ILE* 2.6 40.2 + - + +
171G ARG* 3.2 30.7 - - - +
182H LEU* 3.4 33.9 - - + +
186H VAL* 3.5 27.8 - - + -
124I LEU* 5.2 2.5 - - + -
128I VAL* 4.4 17.5 - - + -
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Residues in contact with ASP 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G GLU* 3.0 25.5 + - - +
152G VAL* 3.4 23.2 - - - +
154G ILE* 1.3 77.5 - - - +
156G ILE* 1.3 66.1 + - - +
158G ILE* 3.6 15.1 - - - +
159G ARG* 3.7 29.7 + - - +
171G ARG* 3.0 28.6 - - - +
173G VAL* 3.9 17.3 - - + +
418H TRP* 5.7 0.5 - - - +
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Residues in contact with ILE 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G VAL* 3.2 14.6 + - + +
153G ASP* 3.3 12.1 - - - +
154G ILE 3.0 0.6 - - - -
155G ASP* 1.3 83.8 + - - +
157G LYS* 1.3 73.7 + - + +
158G ILE 3.2 2.0 - - - -
159G ARG* 3.5 11.9 + - - +
160G SER* 3.4 15.2 + - - -
258H GLY* 5.2 2.3 - - - -
415H ARG* 3.7 32.1 - - + +
416H TYR* 2.8 53.6 - - + +
417H TYR* 4.0 21.1 - - + +
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Residues in contact with LYS 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G ASP* 2.9 54.5 + - - +
154G ILE* 3.0 4.5 + - - +
156G ILE* 1.3 81.5 - - + +
158G ILE* 1.3 62.9 + - + +
159G ARG 3.3 0.2 - - - -
160G SER* 2.8 30.8 + - - -
161G CYS* 3.7 6.9 - - - -
415H ARG* 4.0 10.1 - - - +
428H LYS* 4.6 13.3 - - - +
128I VAL* 4.3 20.4 - - + +
129I ALA* 5.3 7.3 - - - +
131I LEU* 4.3 8.5 - - + +
132I GLU* 3.5 47.2 + - + +
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Residues in contact with ILE 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ILE* 2.6 23.9 + - + +
155G ASP 3.6 9.9 - - - +
156G ILE 3.2 0.2 - - - -
157G LYS* 1.3 72.7 - - + +
159G ARG* 1.3 75.7 + - + +
160G SER 3.2 0.3 + - - -
161G CYS* 3.3 19.6 + - - +
162G ARG* 4.4 3.3 + - - +
168G ALA* 5.6 1.6 - - + +
169G LEU* 5.3 9.2 - - + +
171G ARG* 3.2 47.3 - - + +
185H ASP 4.3 5.4 - - - +
186H VAL* 4.7 2.5 - - + -
189H GLN* 3.4 40.1 - - + +
131I LEU* 3.9 25.8 - - + -
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Residues in contact with ARG 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G ASP* 3.7 31.6 + - - +
156G ILE* 3.5 10.1 + - - +
157G LYS 3.3 0.2 - - - -
158G ILE* 1.3 82.1 - - + +
160G SER* 1.3 49.8 + - - +
161G CYS 2.4 18.8 + - - -
162G ARG* 3.1 21.5 + - + +
171G ARG* 5.3 12.7 + - + +
258H GLY* 3.4 23.8 - - - +
259H SER* 2.4 27.8 + - - +
416H TYR* 4.6 8.9 + - + -
418H TRP* 2.9 72.8 - - - +
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Residues in contact with SER 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G ILE 3.4 4.5 + - - -
157G LYS* 2.8 28.5 + - - -
159G ARG* 1.3 76.1 - - - +
161G CYS* 1.3 58.0 + - - -
258H GLY* 4.4 1.7 - - - -
259H SER 3.4 17.9 - - - +
261H ASP* 2.7 38.7 + - - +
132I GLU* 4.2 10.2 - - - +
135I CYS* 3.0 22.2 - - - +
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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