Contacts of the helix formed by residues 164 - 175 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLY 3.3 34.1 - - - +
134A LEU* 4.5 6.5 - - + -
136A GLY* 6.2 0.9 - - - -
139A LEU* 3.7 17.3 - - + -
162A GLU 3.9 0.8 + - - +
163A VAL* 1.3 80.5 - - - +
165A PRO* 1.3 76.0 - - + +
166A PRO* 3.7 20.9 - - + -
167A TYR* 2.9 25.1 + - + +
168A CYS* 3.2 8.7 + - - -
187A GLY 3.7 12.8 - - - +
188A TYR* 3.9 12.3 - - + -
189A PHE* 4.0 5.8 - - - -
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Residues in contact with PRO 165 (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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164A ILE* 1.3 87.1 - - + +
166A PRO* 1.3 70.9 - - + +
168A CYS* 3.0 22.3 + - + +
169A ALA* 3.4 5.7 + - - +
185A GLU 3.8 21.5 - - - +
186A GLU* 4.4 5.8 - - + -
187A GLY 3.5 15.0 - - - +
189A PHE* 4.0 11.9 - - + -
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Residues in contact with PRO 166 (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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139A LEU* 5.4 0.9 - - + -
164A ILE* 3.5 23.1 - - + -
165A PRO* 1.3 99.9 - - + +
167A TYR* 1.3 59.2 + - - +
169A ALA* 3.1 19.3 + - + +
170A TYR* 3.2 36.9 + - + +
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Residues in contact with TYR 167 (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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131A ILE* 3.6 41.4 + - + +
133A GLY* 4.7 2.0 - - - -
139A LEU* 3.7 35.4 - - + -
142A ARG* 4.2 1.2 + - + -
143A ALA* 3.5 31.6 + - + -
146A VAL* 3.2 32.5 - - + +
160A LEU* 4.8 2.7 - - + -
163A VAL* 4.1 5.4 - - + -
164A ILE* 2.9 28.3 + - + +
166A PRO* 1.3 75.5 - - - +
168A CYS* 1.3 64.8 + - - +
170A TYR* 3.1 10.5 + + - +
171A LEU* 3.0 48.9 + - + +
356A PRO 5.5 0.3 + - - -
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Residues in contact with CYS 168 (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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163A VAL* 3.7 22.0 - - - -
164A ILE 3.2 7.0 + - - -
165A PRO* 3.0 12.8 + - + +
167A TYR* 1.3 76.1 - - - +
169A ALA* 1.3 57.1 + - - +
171A LEU* 3.3 10.9 + - - +
172A LYS* 2.9 47.5 + - - +
180A ILE* 3.8 12.7 - - + +
182A THR* 4.1 15.5 - - - -
189A PHE* 4.1 17.3 - - - -
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Residues in contact with ALA 169 (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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165A PRO 3.4 5.1 + - - +
166A PRO* 3.1 15.8 + - + +
168A CYS* 1.3 80.7 - - - +
170A TYR* 1.3 67.6 + - + +
172A LYS* 3.3 13.8 + - - +
173A LYS* 3.1 21.7 + - - +
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Residues in contact with TYR 170 (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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139A LEU* 4.4 14.4 - - + +
140A PRO* 3.7 40.4 - - + +
143A ALA* 3.8 32.1 - - + -
147A CYS* 5.0 1.6 - - - -
166A PRO* 3.2 31.3 + - + +
167A TYR* 3.1 17.1 + + + +
169A ALA* 1.3 79.7 - - + +
171A LEU* 1.3 53.2 + - + +
173A LYS* 3.2 11.4 + - + +
174A ARG* 2.8 41.1 + - + +
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Residues in contact with LEU 171 (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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146A VAL* 5.1 3.1 - - + -
147A CYS* 3.8 23.3 - - - -
150A LEU* 4.8 4.9 - - + -
160A LEU* 3.7 26.0 - - + -
163A VAL* 4.9 6.1 - - + -
167A TYR* 3.0 40.0 + - + +
168A CYS* 3.5 13.2 - - - +
170A TYR* 1.3 73.4 - - + +
172A LYS* 1.3 60.2 + - - +
173A LYS 3.1 1.6 - - - -
175A ALA* 2.8 41.8 + - + +
180A ILE* 3.9 17.7 - - + -
191A ALA* 5.9 0.2 - - + -
193A LEU* 4.3 24.9 - - + -
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Residues in contact with LYS 172 (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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168A CYS* 2.9 35.5 + - - +
169A ALA* 3.3 10.4 + - - +
171A LEU* 1.3 76.5 - - - +
173A LYS* 1.3 59.1 + - - +
175A ALA 5.0 0.2 - - - -
176A ALA* 3.5 23.4 - - - +
178A TYR 6.1 0.9 - - - -
180A ILE* 3.7 20.9 - - + -
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Residues in contact with LYS 173 (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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169A ALA 3.1 12.1 + - - +
170A TYR* 3.5 13.2 - - + +
171A LEU 3.1 0.4 - - - -
172A LYS* 1.3 79.8 - - - +
174A ARG* 1.3 95.4 + - + +
175A ALA 3.5 0.6 + - - -
176A ALA* 4.5 6.9 + - - +
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Residues in contact with ARG 174 (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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143A ALA 5.9 0.2 - - - -
144A ARG* 3.0 48.4 - - + +
147A CYS* 3.5 38.8 - - + +
151A ALA* 6.0 1.0 - - - +
170A TYR* 2.8 17.1 + - + +
173A LYS* 1.3 112.7 - - + +
175A ALA* 1.3 58.6 + - - +
176A ALA 3.8 0.7 - - - -
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Residues in contact with ALA 175 (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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147A CYS* 4.0 14.6 - - + -
150A LEU* 4.3 13.9 - - + -
171A LEU* 2.8 22.5 + - + +
172A LYS* 5.0 0.3 - - - -
174A ARG* 1.3 80.9 - - - +
176A ALA* 1.3 63.6 + - - +
177A SER* 3.1 5.9 + - - -
178A TYR* 3.1 39.0 + - + +
180A ILE* 5.9 0.7 - - - +
193A LEU* 4.9 1.7 - - + +
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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