Contacts of the helix formed by residues 180 - 193 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B VAL* 4.8 4.0 - - - +
173B LEU* 5.9 0.2 - - - +
179B ALA* 1.3 85.1 + - - +
181B THR* 1.3 62.7 + - - +
182B SER* 3.1 26.7 - - - +
183B SER* 3.1 11.4 + - - -
184B ALA* 2.7 38.1 + - - +
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Residues in contact with THR 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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14A LEU* 3.9 21.9 - - + +
146B ALA 4.1 5.6 - - - +
147B VAL* 3.6 38.7 - - + +
150B PRO* 4.1 15.3 - - + -
151B VAL* 3.5 14.0 - - + +
180B THR* 1.3 77.1 - - - +
182B SER* 1.3 57.5 + - - +
184B ALA* 4.3 0.7 - - - -
185B LEU* 2.8 36.4 + - - +
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.3 11.0 - - - +
32A PRO* 5.3 1.4 + - - +
36A ALA* 4.3 12.0 + - - +
180B THR* 3.0 15.0 - - - -
181B THR* 1.3 80.9 + - - +
183B SER* 1.3 58.7 + - - -
185B LEU* 2.8 24.5 + - - +
186B ARG* 2.9 34.5 + - - +
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Residues in contact with SER 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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172B VAL* 5.2 0.4 - - - -
176B ASN* 4.8 6.6 + - - -
179B ALA* 3.8 10.2 - - - +
180B THR* 3.1 25.7 + - - -
182B SER* 1.3 79.6 + - - +
184B ALA* 1.3 55.6 + - - +
186B ARG* 3.3 27.1 + - - +
187B SER* 2.8 38.3 + - - -
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Residues in contact with ALA 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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147B VAL* 4.7 0.9 - - + -
151B VAL* 3.9 18.3 - - + +
169B THR* 5.4 2.2 - - + -
172B VAL* 3.9 16.8 - - + +
173B LEU* 4.1 25.6 - - + -
179B ALA* 6.2 0.7 - - + -
180B THR 2.7 24.0 + - - +
181B THR* 3.7 3.8 - - - +
183B SER* 1.3 74.0 + - - +
185B LEU* 1.3 58.1 + - - +
187B SER* 3.8 0.5 - - - -
188B ALA* 2.8 31.7 + - - +
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Residues in contact with LEU 185 (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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14A LEU* 3.6 36.3 - - + +
32A PRO* 3.6 22.7 - - + -
151B VAL* 3.7 13.6 - - + +
154B ALA* 3.9 19.3 - - + -
155B LEU* 3.9 19.1 - - + -
158B LEU* 5.0 3.8 - - + -
181B THR 2.8 19.6 + - - +
182B SER* 2.8 6.0 + - - +
184B ALA* 1.3 77.0 - - - +
186B ARG* 1.3 62.7 + - - +
188B ALA* 3.2 2.1 + - - +
189B LEU* 2.9 45.5 + - + +
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Residues in contact with ARG 186 (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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32A PRO* 3.5 28.0 - - + -
33A ALA* 4.1 7.4 - - + +
36A ALA* 3.3 34.3 - - - +
182B SER* 2.9 28.4 + - - +
183B SER* 3.4 31.9 - - - +
185B LEU* 1.3 76.6 - - - +
187B SER* 1.3 61.8 + - - +
189B LEU* 3.6 9.7 + - - +
190B SER* 3.3 19.9 + - - -
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Residues in contact with SER 187 (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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172B VAL* 3.5 28.9 - - - +
183B SER 2.8 21.9 + - - -
186B ARG* 1.3 73.3 - - - +
188B ALA* 1.3 64.7 + - - +
190B SER* 3.3 8.5 + - - -
191B LEU* 3.2 24.3 + - - +
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Residues in contact with ALA 188 (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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151B VAL* 4.6 1.1 - - + -
155B LEU* 3.9 24.2 - - + -
168B ALA* 4.2 15.8 - - + +
169B THR* 4.5 4.9 - - - +
172B VAL* 3.6 15.6 - - + +
184B ALA 2.8 18.8 + - - +
185B LEU* 3.2 5.1 + - - +
187B SER* 1.3 74.6 - - - +
189B LEU* 1.3 60.4 + - - +
191B LEU* 3.3 4.4 + - - +
192B LEU* 2.9 34.4 + - - +
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Residues in contact with LEU 189 (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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32A PRO* 3.4 27.6 - - + -
90A ALA 3.8 23.3 - - - +
91A VAL* 4.5 17.1 - - + +
155B LEU* 3.5 21.3 - - + -
158B LEU* 4.0 16.6 - - + -
160B PHE* 4.1 16.4 - - + -
185B LEU* 2.9 38.4 + - + +
186B ARG* 3.8 6.5 - - - +
188B ALA* 1.3 76.2 - - - +
190B SER* 1.3 56.5 + - - +
192B LEU* 3.6 4.7 - - - +
193B GLY* 2.9 25.8 + - - -
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Residues in contact with SER 190 (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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91A VAL 5.9 1.3 - - - -
186B ARG 3.3 11.3 + - - -
187B SER* 3.3 13.2 - - - -
188B ALA 3.2 0.4 - - - -
189B LEU* 1.3 74.7 - - - +
191B LEU* 1.3 68.9 + - - +
193B GLY* 3.0 14.3 + - - -
194B LYS 3.7 5.0 + - - -
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Residues in contact with LEU 191 (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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168B ALA* 3.8 32.1 - - + +
171B THR* 3.9 22.4 - - + +
172B VAL* 3.9 15.0 - - + -
187B SER* 3.2 11.0 + - - +
188B ALA 3.3 5.1 + - - +
190B SER* 1.3 78.2 + - - +
192B LEU* 1.3 54.4 + - + +
194B LYS* 2.6 33.1 + - - -
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Residues in contact with LEU 192 (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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91A VAL* 5.1 1.9 - - - +
111A ARG* 4.1 16.1 - - - +
155B LEU* 3.7 34.3 - - + -
160B PHE* 3.4 43.4 - - + -
164B GLN* 3.8 35.9 - - + +
165B ALA* 5.3 1.6 - - - -
168B ALA* 3.9 18.4 - - + -
188B ALA 2.9 21.7 + - - +
189B LEU* 3.6 5.4 - - - +
191B LEU* 1.3 70.2 - - + +
193B GLY* 1.3 57.5 + - - +
194B LYS* 2.8 11.4 + - - +
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Residues in contact with GLY 193 (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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91A VAL* 4.2 21.5 - - - -
92A HIS* 4.6 8.7 + - - -
111A ARG* 3.4 17.9 + - - -
189B LEU 2.9 14.8 + - - -
190B SER* 3.0 7.4 + - - -
191B LEU 3.0 1.6 + - - -
192B LEU* 1.3 74.0 - - - +
194B LYS* 1.3 69.7 + - - +
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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