Contacts of the helix formed by residues 164 - 176 (chain A) in PDB entry 5I1U
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 ASP 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A PRO* 1.3 77.2 - - - +
165A ARG* 1.3 64.7 + - - +
166A GLU* 3.3 9.4 + - - +
167A GLY* 2.7 31.2 + - - -
168A TYR* 2.9 22.5 + - - +
238A ILE* 4.6 0.2 - - - -
241A ARG* 4.7 6.7 - - - +
242A ASP* 5.8 0.2 - - - -
205B GLN* 5.5 0.9 + - - -
264B ARG* 3.3 23.3 + - - +
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Residues in contact with ARG 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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163A PRO 4.0 0.6 + - - -
164A ASP* 1.3 73.8 - - - +
166A GLU* 1.3 78.6 + - + +
168A TYR* 3.3 5.0 + - - +
169A LEU* 2.9 53.9 + - + +
216A PHE* 3.9 27.9 - - - -
235A LEU* 3.9 22.5 - - + +
238A ILE* 4.0 21.8 - - + +
239A VAL* 4.1 16.8 - - - +
242A ASP* 4.9 5.7 + - - +
253A VAL* 5.7 3.4 - - - +
254A VAL* 5.9 0.4 - - - +
257A GLU* 4.4 12.3 - - - +
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Residues in contact with GLU 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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164A ASP* 3.4 12.0 - - - +
165A ARG* 1.3 96.6 + - + +
167A GLY* 1.3 54.8 + - - +
169A LEU* 3.5 5.5 + - - +
170A THR* 2.7 39.2 + - - +
205B GLN* 3.4 18.2 - - + +
264B ARG* 3.7 20.4 + - - +
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Residues in contact with GLY 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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163A PRO* 5.3 2.5 - - - -
164A ASP* 2.7 24.9 + - - -
166A GLU* 1.3 72.9 - - - +
168A TYR* 1.3 61.7 + - - +
170A THR* 3.4 1.2 + - - -
171A LEU* 3.0 24.9 + - - +
201B PRO* 3.6 11.6 - - - +
205B GLN* 3.5 20.3 - - - +
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Residues in contact with TYR 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 PRO* 3.9 22.9 - - + +
164A ASP 2.9 17.9 + - - +
165A ARG 3.6 2.5 - - - +
167A GLY* 1.3 76.4 - - - +
169A LEU* 1.3 74.7 + - + +
171A LEU* 3.3 12.1 + - + +
172A ARG* 2.8 52.4 + - + +
219A ASP* 2.7 38.1 + - - -
233A ALA* 3.3 37.5 + - + -
234A ASN* 3.9 0.2 - - - -
235A LEU* 3.8 14.1 - - + -
238A ILE* 3.7 20.4 - - + -
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Residues in contact with LEU 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 ARG* 2.9 49.7 + - + +
166A GLU* 4.1 5.2 - - - +
168A TYR* 1.3 92.4 - - + +
170A THR* 1.3 65.4 + - - +
172A ARG* 3.8 7.9 - - + +
173A ARG* 3.0 35.6 + - + +
215A SER* 5.0 4.9 - - - +
216A PHE* 4.0 34.8 - - + -
235A LEU* 4.4 9.0 - - + -
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Residues in contact with THR 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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145A TYR* 4.4 4.2 + - - -
149A CYS* 5.3 0.9 - - - -
166A GLU* 2.7 23.7 + - - +
167A GLY 3.7 4.0 - - - -
169A LEU* 1.3 78.4 - - - +
171A LEU* 1.3 62.4 + - - +
173A ARG* 3.6 14.9 + - - +
174A GLY* 3.8 5.9 + - - -
201B PRO* 3.7 28.9 - - + +
204B ARG* 3.7 38.9 + - + +
205B GLN* 3.6 16.1 - - + +
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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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149A CYS* 3.6 33.8 - - + +
152A ALA* 4.2 12.8 - - + +
153A GLU* 3.3 38.6 - - - +
156A GLY* 6.3 1.1 - - - -
167A GLY 3.0 17.2 + - - +
168A TYR* 3.6 10.8 - - + +
170A THR* 1.3 77.8 - - - +
172A ARG* 1.3 64.9 + - - +
174A GLY* 3.0 12.6 + - - -
175A THR* 3.0 24.2 + - + +
199B HIS 6.1 0.4 - - - -
201B PRO* 3.9 18.8 - - + +
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Residues in contact with ARG 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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153A GLU* 5.8 0.8 + - - -
168A TYR* 2.8 51.6 + - + +
169A LEU* 3.8 12.3 - - + +
170A THR 3.4 0.2 - - - -
171A LEU* 1.3 74.5 - - - +
173A ARG* 1.3 61.6 + - + +
175A THR* 3.0 26.4 + - - -
176A ALA* 2.9 55.3 + - - +
215A SER* 3.8 34.2 + - - +
218A ASN* 4.4 16.0 + - - +
219A ASP* 5.0 4.6 + - - -
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Residues in contact with ARG 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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145A TYR* 3.5 21.3 + - - +
169A LEU* 3.0 28.4 + - + +
170A THR* 3.9 8.2 - - - +
171A LEU 3.2 0.4 - - - -
172A ARG* 1.3 77.7 - - + +
174A GLY* 1.3 60.5 + - - +
176A ALA* 4.0 7.9 + - - +
177A ALA* 4.1 6.2 + - - -
178A MET* 4.6 6.4 + - - +
179A GLU* 5.4 3.3 + - - +
208A GLN* 3.3 31.7 + - - +
211A ALA* 6.3 0.2 - - + -
212A ASP* 2.8 43.6 + - - +
215A SER* 6.5 0.4 - - - -
204B ARG* 5.8 4.9 - - - +
401B SO4 3.2 41.4 + - - -
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Residues in contact with GLY 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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145A TYR* 3.5 31.3 + - - -
146A TYR* 3.6 18.9 + - - +
149A CYS* 3.7 12.6 - - - -
170A THR 3.8 2.8 + - - -
171A LEU 3.0 7.4 + - - -
173A ARG* 1.3 78.4 - - - +
175A THR* 1.3 65.3 + - - +
177A ALA* 3.3 11.6 + - - -
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Residues in contact with THR 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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146A TYR* 3.5 21.8 - - - -
149A CYS* 3.8 24.7 - - + +
150A HIS* 4.7 12.7 + - + +
153A GLU* 4.5 21.1 + - + +
171A LEU* 3.0 24.8 + - + +
172A ARG* 3.0 33.4 + - - -
174A GLY* 1.3 75.7 - - - +
176A ALA* 1.3 61.5 + - - +
177A ALA 3.2 1.1 + - - -
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Residues in contact with ALA 176 (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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172A ARG* 2.9 41.6 + - + +
173A ARG* 4.2 5.8 - - - +
174A GLY 3.2 0.2 - - - -
175A THR* 1.3 77.9 + - - +
177A ALA* 1.3 67.2 + - - +
178A MET* 3.1 24.3 + - + +
181A ILE* 3.9 10.2 - - - +
211A ALA 5.5 0.9 - - - +
215A SER* 5.3 5.8 - - - -
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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