Contacts of the helix formed by residues 180 - 194 (chain C) in PDB entry 2H5X
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 THR 180 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179C ALA* 1.3 84.2 - - - +
181C THR* 1.3 65.0 + - - +
182C SER* 3.9 12.6 - - - -
183C SER* 3.2 18.6 + - - -
184C ALA* 3.1 20.4 + - - +
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Residues in contact with THR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 4.0 20.2 - - + +
146C ALA 5.8 0.2 - - - -
147C VAL* 3.8 23.5 + - - +
150C PRO* 4.1 12.7 - - - +
151C VAL* 3.2 28.7 - - - +
179C ALA 3.5 2.1 + - - -
180C THR* 1.3 73.3 - - - +
182C SER* 1.3 67.5 + - - +
184C ALA* 4.2 1.8 - - - -
185C LEU* 3.1 19.2 + - - +
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Residues in contact with SER 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 4.2 13.2 - - - -
32B PRO* 4.5 7.6 + - - +
35B LEU* 5.2 1.9 - - - +
36B ALA* 4.3 12.6 + - - -
180C THR* 4.3 8.1 - - - -
181C THR* 1.3 81.3 - - - +
183C SER* 1.3 57.4 + - - +
184C ALA 3.0 1.1 - - - -
185C LEU* 2.7 26.4 + - - +
186C ARG* 2.9 30.1 + - - +
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ASN* 5.6 3.4 + - - -
179C ALA* 4.4 6.9 - - - +
180C THR* 3.2 25.5 + - - -
182C SER* 1.3 77.6 - - - +
184C ALA* 1.3 52.3 + - - +
186C ARG* 3.2 34.4 - - - +
187C SER* 2.7 39.9 + - - -
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Residues in contact with ALA 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C VAL* 6.0 0.7 - - + -
151C VAL* 4.0 18.1 - - + +
172C VAL* 3.8 9.9 - - + +
173C LEU* 4.0 26.2 - - + -
179C ALA 5.1 0.2 - - - +
180C THR 3.1 18.3 + - - +
181C THR* 3.5 7.2 - - - +
182C SER 3.0 0.8 - - - -
183C SER* 1.3 79.0 + - - +
185C LEU* 1.3 58.3 + - - +
187C SER* 3.6 4.2 - - - -
188C ALA* 2.8 30.8 + - - +
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Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 3.4 34.8 - - + +
32B PRO* 3.6 20.6 - - + -
151C VAL* 3.7 13.9 - - + +
154C ALA* 3.4 24.2 - - + +
155C LEU* 3.6 22.4 - - + -
158C LEU* 5.0 2.7 - - + -
181C THR 3.1 12.7 + - - +
182C SER* 2.7 11.4 + - - +
184C ALA* 1.3 74.0 - - - +
186C ARG* 1.3 57.8 + - - +
187C SER 3.0 4.3 - - - -
188C ALA* 3.3 1.9 + - - +
189C LEU* 3.0 43.5 + - + +
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Residues in contact with ARG 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PRO* 3.8 17.7 - - + +
33B ALA* 4.3 15.9 - - + +
36B ALA* 3.5 29.5 - - - +
182C SER* 2.9 35.1 + - - +
183C SER* 3.2 35.6 - - - +
185C LEU* 1.3 77.1 - - - +
187C SER* 1.3 61.3 + - - +
189C LEU* 3.7 13.5 - - + +
190C SER* 3.4 19.8 + - - -
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C VAL* 3.6 24.4 - - - +
176C ASN* 6.2 0.2 - - - +
183C SER 2.7 21.4 + - - -
184C ALA* 3.6 6.7 - - - -
186C ARG* 1.3 78.2 - - - +
188C ALA* 1.3 63.9 + - - +
189C LEU 3.1 1.1 - - - -
190C SER* 3.3 7.7 + - - -
191C LEU* 3.3 22.0 + - - +
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Residues in contact with ALA 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C VAL* 4.6 0.4 - - + -
155C LEU* 3.9 24.9 - - + -
168C ALA* 3.9 16.2 - - + +
169C THR* 4.1 12.6 - - - +
172C VAL* 3.8 9.4 - - + +
184C ALA 2.8 18.1 + - - +
185C LEU* 3.7 5.8 - - - +
187C SER* 1.3 78.2 - - - +
189C LEU* 1.3 57.9 + - - +
191C LEU* 3.4 3.3 + - - +
192C LEU* 2.9 34.9 + - - +
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Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PRO* 3.7 21.1 - - + -
90B ALA 3.5 25.4 - - - +
91B VAL* 4.5 13.5 - - + +
155C LEU* 3.5 22.2 - - + -
158C LEU* 4.1 12.8 - - + -
160C PHE* 3.7 24.2 - - + -
185C LEU* 3.0 40.3 + - + +
186C ARG* 3.7 10.1 - - - +
187C SER 3.1 0.2 - - - -
188C ALA* 1.3 75.3 - - - +
190C SER* 1.3 65.9 + - - +
192C LEU* 3.2 3.5 + - + +
193C GLY* 2.9 20.8 + - - -
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Residues in contact with SER 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B VAL 5.4 3.4 - - - -
186C ARG 3.4 11.8 + - - -
187C SER* 3.3 11.3 + - - -
189C LEU* 1.3 77.9 - - - +
191C LEU* 1.3 68.9 + - - +
193C GLY* 3.3 7.7 + - - -
194C LYS* 3.5 12.3 + - - +
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Residues in contact with LEU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ALA* 4.4 9.2 - - + +
171C THR* 3.5 38.1 - - + +
172C VAL* 4.1 13.9 - - + -
187C SER* 3.3 16.5 + - - +
188C ALA* 3.7 7.4 - - - +
189C LEU 3.2 0.4 - - - -
190C SER* 1.3 79.9 - - - +
192C LEU* 1.3 55.3 + - - +
193C GLY 2.7 16.7 + - - -
194C LYS* 3.0 19.8 + - - +
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B VAL* 4.6 2.7 - - - +
111B ARG* 4.5 12.5 - - - +
155C LEU* 3.8 36.8 - - + -
160C PHE* 3.7 44.8 - - + -
164C GLN* 3.2 44.6 - - + +
165C ALA* 4.8 0.2 - - - -
168C ALA* 3.7 13.5 - - + -
188C ALA 2.9 21.2 + - - +
189C LEU* 3.2 6.5 + - + +
191C LEU* 1.3 74.3 - - - +
193C GLY* 1.3 57.5 + - - +
194C LYS 5.3 0.6 - - - -
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Residues in contact with GLY 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B VAL* 3.8 23.1 - - - -
92B HIS* 4.1 9.6 + - - -
111B ARG* 3.3 25.8 + - - -
189C LEU 2.9 12.4 + - - -
190C SER* 3.3 3.8 + - - -
191C LEU 2.7 8.5 + - - -
192C LEU* 1.3 75.4 - - - +
194C LYS* 1.3 57.8 + - - -
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Residues in contact with LYS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG* 4.0 28.1 + - - +
190C SER 3.5 8.7 + - - +
191C LEU* 3.0 13.2 + - - +
192C LEU 5.3 1.1 - - - -
193C GLY* 1.3 79.6 - - - +
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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