Contacts of the helix formed by residues 179 - 188 (chain A) in PDB entry 2H6C
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 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A LEU* 1.3 77.2 - - - +
180A GLN* 1.3 57.7 + - - +
181A LYS* 3.5 12.7 + - - +
182A SER* 2.7 43.8 + - - -
183A ILE* 2.9 27.5 + - - +
209A LYS* 4.9 2.7 - - - +
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Residues in contact with GLN 180 (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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178A LEU 3.7 1.5 + - - +
179A SER* 1.3 72.2 - - - +
181A LYS* 1.3 53.0 + - - +
183A ILE* 3.2 7.8 + - + +
184A GLY* 2.7 31.2 + - - -
191A HIS* 4.2 8.1 + - + +
194A VAL* 3.4 29.3 - - + +
195A SER* 3.2 29.8 + - - +
198A LEU* 3.2 27.0 - - + +
209A LYS* 5.4 6.3 - - - +
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Residues in contact with LYS 181 (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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69A ASP* 4.4 19.8 + - - -
71A SER* 5.7 5.7 + - - -
179A SER* 3.5 10.7 - - - +
180A GLN* 1.3 76.6 - - - +
182A SER* 1.3 51.3 + - - +
184A GLY* 3.0 3.9 + - - -
185A GLU* 2.6 65.7 + - + +
191A HIS* 6.6 0.4 - - - -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 4.1 11.2 - - - -
179A SER* 2.7 38.0 + - - -
181A LYS* 1.3 72.9 - - - +
183A ILE* 1.3 56.8 + - - +
185A GLU* 3.6 14.7 + - - +
186A ILE* 2.8 38.4 + - - +
155B ARG* 5.4 1.8 - - - -
159B GLU* 2.9 30.0 + - - -
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Residues in contact with ILE 183 (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 ILE* 3.7 31.9 - - + -
156A LEU* 4.2 15.9 - - + -
157A PHE* 4.0 20.2 - - + -
178A LEU* 3.7 40.2 - - + +
179A SER 2.9 20.1 + - - +
180A GLN* 3.4 11.7 - - - +
181A LYS 3.1 0.2 - - - -
182A SER* 1.3 76.9 - - - +
184A GLY* 1.3 59.0 + - - +
186A ILE* 3.2 4.3 + - - -
187A THR* 2.9 33.8 + - + +
194A VAL* 4.1 11.2 - - + -
198A LEU* 5.5 5.4 - - + -
209A LYS* 4.8 4.9 - - + -
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Residues in contact with GLY 184 (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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180A GLN 2.7 18.4 + - - -
181A LYS* 3.5 2.5 - - - -
183A ILE* 1.3 71.8 - - - +
185A GLU* 1.3 61.0 + - - +
187A THR* 3.9 4.3 - - - -
188A GLY* 2.7 32.2 + - - -
189A ALA 3.3 22.7 + - - -
191A HIS* 6.1 0.2 - - - -
194A VAL* 4.0 6.3 - - - +
145B ASN* 5.1 3.8 - - - +
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Residues in contact with GLU 185 (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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181A LYS* 2.6 59.5 + - + +
182A SER* 3.6 15.3 + - - +
184A GLY* 1.3 72.8 - - - +
186A ILE* 1.3 58.0 + - - +
188A GLY* 4.0 0.9 + - - -
148B ASN* 5.1 4.0 - - - +
151B ILE* 5.1 2.3 - - - +
152B ARG* 3.1 24.8 - - - +
155B ARG* 3.3 47.8 + - - +
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Residues in contact with ILE 186 (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 LEU* 4.7 9.2 - - + -
178A LEU* 5.0 4.9 - - + -
182A SER* 2.8 25.3 + - - +
183A ILE* 3.7 5.6 - - - +
184A GLY 3.2 0.2 - - - -
185A GLU* 1.3 80.1 - - - +
187A THR* 1.3 60.4 + - + +
152B ARG* 3.1 24.8 - - - +
155B ARG* 3.9 9.6 - - + +
156B LEU* 3.8 47.8 - - + +
159B GLU* 4.3 19.5 - - + -
186B ILE* 3.8 26.7 - - + -
187B THR* 3.6 13.6 - - + +
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Residues in contact with THR 187 (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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149A PRO 4.5 2.2 - - - -
152A ARG* 2.4 57.0 + - - +
153A ILE* 4.2 15.3 - - + +
156A LEU* 4.6 10.5 - - + -
183A ILE* 2.9 18.6 + - + +
184A GLY* 3.9 0.2 - - - -
186A ILE* 1.3 82.5 - - + +
188A GLY* 1.3 55.9 + - - +
189A ALA* 3.3 23.3 + - - +
152B ARG* 3.9 4.9 - - - +
186B ILE* 3.7 21.8 - - + +
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Residues in contact with GLY 188 (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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149A PRO* 4.2 4.5 - - - +
152A ARG* 4.0 7.0 + - - -
184A GLY 2.7 14.6 + - - -
185A GLU 4.7 1.3 - - - -
186A ILE 3.5 2.0 - - - -
187A THR* 1.3 78.7 - - - +
189A ALA* 1.3 56.2 + - - -
190A HIS 4.3 0.2 + - - -
145B ASN* 4.5 19.9 - - - +
148B ASN* 5.1 1.3 - - - -
152B ARG* 3.6 24.7 + - - +
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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