Contacts of the helix formed by residues 176 - 184 (chain B) in PDB entry 4HH3
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 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 3.2 35.6 + - + +
156B ASP* 4.5 7.6 - - - +
158B SER* 3.1 23.1 + - - +
160B ASP 3.0 24.0 + - - -
161B PRO* 3.6 0.7 - - - +
162B MET* 3.1 23.0 + - - +
175B LEU* 1.3 80.7 - - - +
177B SER* 1.3 66.5 + - - +
178B ALA* 4.0 4.7 - - - +
179B ALA* 3.1 15.8 + - - +
180B GLY* 3.0 17.0 + - - -
187B ARG* 4.8 5.6 - - - +
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ASP* 4.8 17.0 + - - -
176B ASN* 1.3 74.6 - - - +
178B ALA* 1.3 64.0 + - - +
180B GLY* 3.6 3.0 - - - +
181B LEU* 3.0 31.9 + - - +
187B ARG* 5.2 11.3 - - - +
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B SER 4.6 1.1 + - - +
159B ARG* 3.6 31.4 - - - +
161B PRO* 3.9 14.7 - - + +
176B ASN* 3.2 11.3 + - - +
177B SER* 1.3 82.9 + - - +
179B ALA* 1.3 60.8 + - - +
181B LEU* 3.5 12.3 + - - +
182B LEU* 3.5 22.5 + - - +
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PRO* 3.7 9.3 - - + +
162B MET 3.4 31.6 - - - +
163B VAL* 3.6 21.1 - - + -
175B LEU* 4.2 4.0 - - + -
176B ASN* 3.1 14.4 + - - +
178B ALA* 1.3 73.6 - - - +
180B GLY* 1.3 67.7 + - - +
182B LEU* 3.1 6.3 + - - +
183B LEU* 2.9 26.6 + - - +
253B ILE* 4.6 4.4 - - + +
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Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B LEU* 3.9 12.9 - - - +
176B ASN 3.0 13.8 + - - -
177B SER* 3.2 6.2 + - - -
179B ALA* 1.3 76.6 - - - +
181B LEU* 1.3 56.6 + - - +
183B LEU 3.3 0.2 + - - -
184B GLY 2.8 27.2 + - - -
185B GLY 3.1 28.4 + - - -
187B ARG 5.1 2.5 - - - -
190B LEU* 4.2 3.4 - - - -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B SER* 3.0 19.6 + - - +
178B ALA* 3.7 13.0 - - - +
179B ALA 3.2 0.4 - - - -
180B GLY* 1.3 77.2 - - - +
182B LEU* 1.3 65.0 + - + +
184B GLY* 3.5 9.3 + - - -
230B SER* 4.5 0.2 - - - -
232B LYS* 3.8 14.4 - - - -
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PRO* 3.8 20.4 - - + -
178B ALA 3.5 7.6 + - - +
179B ALA* 3.1 8.1 + - - +
181B LEU* 1.3 79.2 - - + +
183B LEU* 1.3 53.8 + - - +
230B SER* 2.7 26.0 + - - -
232B LYS* 3.4 25.2 - - + +
234B LEU* 3.9 26.4 - - + +
253B ILE* 3.8 37.0 - - + +
254B ASP 4.3 0.2 - - - -
255B PRO* 4.1 29.6 - - + -
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B VAL* 3.9 27.4 - - + -
172B ILE* 4.7 8.7 - - + -
175B LEU* 4.5 4.0 - - + -
179B ALA 2.9 17.1 + - - +
182B LEU* 1.3 77.1 - - + +
184B GLY* 1.3 58.2 + - - +
190B LEU* 4.0 34.3 - - + -
195B ILE* 5.4 2.7 - - + -
198B GLU* 4.8 10.6 - - + +
199B PHE* 3.7 35.0 - - + -
227B ALA* 4.0 8.7 - - + +
229B ARG* 3.2 23.3 + - - +
230B SER* 3.3 8.7 + - - -
234B LEU* 4.1 11.4 - - + -
253B ILE* 4.4 8.3 - - + -
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Residues in contact with GLY 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B GLY 2.8 10.1 + - - -
181B LEU* 3.5 5.8 + - - -
182B LEU 3.3 2.2 - - - -
183B LEU* 1.3 79.8 - - - +
185B GLY* 1.3 54.6 + - - -
229B ARG* 3.5 17.8 - - - +
230B SER* 3.6 20.4 - - - -
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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