Contacts of the helix formed by residues 164 - 175 (chain B) in PDB entry 5INQ
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 ILE 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLY* 3.3 35.0 - - - +
134B LEU* 4.2 8.3 - - + -
139B LEU* 3.8 16.8 - - + -
162B GLU 3.9 0.4 + - - -
163B VAL* 1.3 77.7 - - - +
165B PRO* 1.3 73.8 - - + +
166B PRO* 3.8 20.2 - - + -
167B TYR* 2.9 17.0 + - + +
168B CYS* 2.8 26.0 + - - +
187B GLY 3.6 13.0 - - - +
188B TYR* 3.9 11.0 - - + -
189B PHE* 3.9 3.4 - - - -
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Residues in contact with PRO 165 (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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164B ILE* 1.3 87.4 - - + +
166B PRO* 1.3 66.5 - - + +
168B CYS* 3.2 9.5 + - + +
169B ALA* 2.8 28.2 + - - +
185B GLU 3.6 24.0 - - - +
186B GLU* 4.6 8.1 - - - +
187B GLY 3.4 16.6 - - - +
189B PHE* 3.9 8.5 - - + -
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Residues in contact with PRO 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 5.7 2.2 - - + -
164B ILE* 3.5 23.3 - - + -
165B PRO* 1.3 98.6 - - + +
167B TYR* 1.3 56.0 + - - +
169B ALA* 3.4 8.8 + - + +
170B TYR* 3.0 26.0 + - - +
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Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 3.6 40.7 + - + +
133B GLY* 4.5 4.9 - - - -
139B LEU* 3.9 31.6 - - + +
142B ARG* 4.6 0.8 - - + -
143B ALA* 3.4 35.2 + - + -
146B VAL* 3.3 33.9 - - + +
160B LEU* 5.3 0.9 - - + -
163B VAL* 4.2 2.5 - - + -
164B ILE* 2.9 22.8 + - + +
166B PRO* 1.3 77.1 - - - +
168B CYS* 1.3 61.0 + - - +
170B TYR* 3.2 8.1 + + - +
171B LEU* 3.0 52.9 + - + +
356B PRO 5.6 0.2 + - - -
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Residues in contact with CYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 3.7 15.1 - - + +
164B ILE 2.8 11.9 + - - +
165B PRO* 3.4 9.6 - - + +
167B TYR* 1.3 74.5 - - - +
169B ALA* 1.3 65.1 + - - +
171B LEU* 3.2 7.4 + - - +
172B LYS* 3.1 44.2 + - - +
180B ILE* 4.8 5.6 - - - -
182B THR* 3.7 30.5 - - - -
189B PHE* 4.1 11.9 - - + -
191B ALA* 6.0 0.2 - - - -
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PRO 2.8 16.1 + - - +
166B PRO* 3.5 13.2 - - + +
168B CYS* 1.3 74.3 - - - +
170B TYR* 1.3 64.3 + - - +
172B LYS* 3.4 16.9 + - - +
173B LYS* 3.5 17.0 + - - +
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Residues in contact with TYR 170 (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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143B ALA* 3.7 29.4 - - + -
144B ARG* 3.5 34.7 - - + +
147B CYS* 3.7 22.0 - - - +
166B PRO 3.0 14.0 + - - +
167B TYR* 3.3 11.9 - + - +
169B ALA* 1.3 76.1 - - - +
171B LEU* 1.3 66.2 + - + +
173B LYS* 3.1 9.6 + - + +
174B ARG* 2.9 63.0 + - + +
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Residues in contact with LEU 171 (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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146B VAL* 5.6 0.9 - - + -
147B CYS* 3.6 31.2 - - - -
150B LEU* 5.4 2.5 - - + -
160B LEU* 3.5 33.2 - - + -
163B VAL* 4.6 11.4 - - + -
167B TYR* 3.0 39.9 + - + +
168B CYS* 3.2 9.2 + - - +
170B TYR* 1.3 78.4 - - + +
172B LYS* 1.3 57.7 + - - +
174B ARG* 4.5 0.4 - - - -
175B ALA* 2.7 43.8 + - + +
180B ILE* 3.4 17.1 - - + +
191B ALA* 5.6 3.1 - - + -
193B LEU* 4.9 10.1 - - + -
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Residues in contact with LYS 172 (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 CYS* 3.1 36.1 + - - +
169B ALA* 3.7 13.0 - - - +
170B TYR 3.3 0.6 - - - -
171B LEU* 1.3 75.4 - - - +
173B LYS* 1.3 59.7 + - + +
176B ALA* 3.3 23.7 - - - +
180B ILE* 3.5 29.6 - - + -
182B THR* 5.6 2.7 - - - -
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Residues in contact with LYS 173 (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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169B ALA 3.5 11.6 + - - +
170B TYR* 3.1 11.3 + - + +
171B LEU 3.1 0.6 - - - -
172B LYS* 1.3 80.6 - - + +
174B ARG* 1.3 65.4 + - - +
175B ALA 3.3 0.2 - - - -
176B ALA* 3.3 16.9 - - - +
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Residues in contact with ARG 174 (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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144B ARG* 5.3 1.0 + - - +
147B CYS* 3.8 42.7 + - + +
148B SER* 4.4 11.1 + - - +
151B ALA* 4.6 10.0 - - - +
170B TYR* 2.9 56.8 + - + +
171B LEU* 4.4 0.7 - - - +
173B LYS* 1.3 75.5 - - - +
175B ALA* 1.3 59.1 + - + +
176B ALA 3.3 1.8 + - - -
177B SER* 4.9 2.4 + - - -
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Residues in contact with ALA 175 (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 CYS* 5.7 1.8 - - - -
150B LEU* 6.1 2.9 - - + -
171B LEU* 2.7 30.0 + - + +
172B LYS 4.6 0.2 - - - -
174B ARG* 1.3 73.3 - - + +
176B ALA* 1.3 52.1 + - - +
177B SER* 2.9 11.4 - - - +
178B TYR* 2.7 42.6 + - + +
180B ILE* 4.1 2.9 - - + +
193B LEU* 3.9 27.4 - - + -
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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