Contacts of the helix formed by residues 178 - 191 (chain B) in PDB entry 2I10
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 PRO 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ARG* 3.9 15.9 - - - +
176B GLY 3.4 4.5 - - - +
177B ALA* 1.4 88.5 - - + +
179B ARG* 1.3 61.2 + - - +
180B GLU* 4.7 2.2 - - + +
181B GLU* 3.4 26.4 + - + +
182B LEU* 3.0 25.1 + - - +
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Residues in contact with ARG 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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93B VAL* 4.2 4.7 + - - +
94B GLU* 3.3 33.4 + - - +
97B THR* 2.7 57.7 + - + +
177B ALA 3.5 2.5 + - - -
178B PRO* 1.3 70.2 - - - +
180B GLU* 1.3 69.0 + - + +
182B LEU* 3.2 2.7 + - - +
183B THR* 2.9 45.1 + - - -
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Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PRO* 3.5 2.3 - - + +
179B ARG* 1.3 83.7 - - + +
181B GLU* 1.3 57.2 + - - +
183B THR* 3.5 6.9 + - - +
184B ALA* 3.0 28.6 + - - +
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Residues in contact with GLU 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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133A ARG* 4.5 5.1 + - - -
156A THR* 3.2 36.7 - - + +
157A ALA* 4.5 5.6 - - + +
160A ARG* 2.7 53.8 + - + +
178B PRO* 3.4 28.1 + - + +
180B GLU* 1.3 80.1 - - - +
182B LEU* 1.3 56.8 + - - +
184B ALA* 3.3 7.6 + - - +
185B ALA* 2.9 26.7 + - - +
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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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160A ARG* 3.7 19.5 - - + +
93B VAL* 3.9 21.5 - - + +
96B PHE* 5.4 0.2 - - + -
97B THR* 4.4 4.7 - - + -
169B LEU* 3.4 43.4 - - + +
172B GLU* 3.6 25.1 - - + -
173B ALA* 3.5 28.7 - - + +
177B ALA* 4.2 5.1 - - + +
178B PRO 3.0 17.4 + - - +
179B ARG* 3.2 5.6 + - - +
181B GLU* 1.3 74.0 - - - +
183B THR* 1.3 60.0 + - - +
185B ALA* 3.2 4.4 + - + +
186B ALA* 2.9 27.9 + - - +
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Residues in contact with THR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR* 4.8 14.6 + - + -
93B VAL* 3.5 18.8 - - - +
94B GLU* 5.8 1.9 - - - +
179B ARG* 2.9 28.2 + - - -
180B GLU* 3.7 7.4 - - - +
182B LEU* 1.3 74.3 - - - +
184B ALA* 1.3 63.9 + - - +
186B ALA* 3.2 6.1 + - - +
187B ILE* 3.0 38.4 + - + +
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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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154A ASP* 4.9 5.2 - - - +
157A ALA* 3.6 26.2 - - + -
180B GLU 3.0 18.6 + - - +
181B GLU* 3.6 3.6 - - - +
182B LEU 3.3 0.2 - - - -
183B THR* 1.3 75.9 - - - +
185B ALA* 1.3 60.8 + - - +
187B ILE* 3.3 12.3 + - - +
188B LEU* 3.0 25.1 + - - +
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Residues in contact with ALA 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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157A ALA* 4.0 9.8 - - - +
160A ARG* 4.1 10.5 - - + -
161A TYR* 3.8 34.6 - - + +
169B LEU* 4.2 11.7 - - + -
181B GLU 2.9 14.8 + - - +
182B LEU 3.2 9.6 + - - +
184B ALA* 1.3 76.7 - - - +
186B ALA* 1.3 56.1 + - - +
188B LEU* 3.3 4.6 + - - +
189B ALA* 2.8 28.4 + - - +
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Residues in contact with ALA 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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86B LEU* 4.8 0.2 - - - +
89B LEU* 3.9 21.4 - - + +
90B THR* 4.2 8.3 - - + +
93B VAL* 3.8 12.1 - - + -
169B LEU* 3.8 28.0 - - + +
182B LEU 2.9 15.9 + - - +
183B THR* 3.2 7.8 + - - +
185B ALA* 1.3 69.5 - - - +
187B ILE* 1.3 60.1 + - - +
189B ALA* 3.2 4.4 + - - +
190B ALA* 2.9 29.5 + - - +
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Residues in contact with ILE 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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82B HIS* 5.3 1.0 - - - -
86B LEU* 3.9 26.5 - - + +
90B THR* 4.1 8.1 - - + -
183B THR* 3.0 32.3 + - + +
184B ALA* 3.3 11.6 + - - +
186B ALA* 1.3 72.8 - - - +
188B LEU* 1.3 66.4 + - + +
190B ALA* 3.4 10.4 + - - +
191B GLN* 3.5 20.5 + - + +
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Residues in contact with LEU 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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154A ASP* 5.1 1.8 - - + +
157A ALA* 3.8 30.1 - - + +
158A LEU* 3.8 32.1 - - + +
161A TYR* 4.2 8.3 - - + -
192A VAL* 3.9 22.6 - - + +
184B ALA* 3.0 19.3 + - + +
185B ALA 3.6 5.8 - - - +
187B ILE* 1.3 73.9 - - + +
189B ALA* 1.3 66.4 + - - +
191B GLN* 3.2 45.5 + - - +
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Residues in contact with ALA 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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161A TYR* 3.6 17.4 - - + -
89B LEU* 3.9 15.9 - - + -
161B TYR* 2.6 37.5 + - - +
165B ALA* 4.2 10.1 - - + -
169B LEU* 5.1 4.0 - - + -
185B ALA 2.8 17.7 + - - +
186B ALA* 3.2 8.7 + - - +
188B LEU* 1.3 76.7 - - - +
190B ALA* 1.3 62.5 + - - +
191B GLN 3.2 1.2 + - - -
192B VAL 3.3 9.0 + - - -
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B HIS* 3.2 20.4 + - + +
85B VAL* 4.4 5.8 - - + -
86B LEU* 3.7 42.8 - - + +
89B LEU* 4.0 9.1 - - + +
186B ALA 2.9 15.3 + - - +
187B ILE 3.7 6.3 - - - +
188B LEU 3.2 0.4 - - - -
189B ALA* 1.3 76.8 - - - +
191B GLN* 1.3 56.5 + - - +
193B VAL* 2.8 23.8 + - - +
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Residues in contact with GLN 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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192A VAL* 4.3 17.2 - - + +
82B HIS* 4.1 11.6 - - + -
187B ILE* 3.5 12.3 + - + +
188B LEU* 3.2 44.3 + - - +
189B ALA 3.1 0.2 - - - -
190B ALA* 1.3 77.4 - - - +
192B VAL* 1.3 60.1 + - - +
193B VAL 3.2 8.2 + - - +
194B PRO* 4.3 3.6 - - - +
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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