Contacts of the helix formed by residues 170 - 178 (chain A) in PDB entry 5X6E
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 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ASN* 2.5 24.9 + - - -
169A LEU* 1.3 73.7 - - - +
171A MET* 1.3 54.6 + - - +
172A GLN* 3.6 19.3 - - + +
173A GLU* 3.0 16.8 + - - +
174A LEU* 2.7 34.0 + - - +
7D C 4.2 33.0 + - - +
8D A 3.2 24.0 - - - +
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Residues in contact with MET 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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169A LEU 3.6 1.3 + - - +
170A THR* 1.3 71.0 - - - +
172A GLN* 1.3 57.0 + - - +
174A LEU* 3.2 6.0 + - - -
175A GLY 2.9 22.0 + - - -
183A SER* 3.6 15.9 - - - +
186A VAL* 3.1 24.1 - - + +
187A SER* 3.5 21.5 - - - +
190A ILE* 3.4 35.0 - - + -
201A TYR* 4.8 10.3 - - - -
206A PHE* 4.6 14.1 - - - -
8D A 2.9 45.0 + - + +
9D T 3.4 23.1 - - - +
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Residues in contact with GLN 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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170A THR* 3.6 13.3 - - + +
171A MET* 1.3 77.5 - - - +
173A GLU* 1.3 53.2 + - - +
175A GLY* 2.9 3.2 + - - -
176A TYR* 2.8 76.4 + - + +
180A ILE 4.4 0.5 - - - +
181A ALA 3.2 25.4 + - - +
182A HIS* 4.0 0.8 - - - +
183A SER* 3.5 31.7 + - - +
186A VAL* 5.2 0.2 - - - -
7D C 5.9 2.0 - - - +
8D A 4.1 0.6 + - - -
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Residues in contact with GLU 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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47A LYS* 2.8 36.7 + - - +
59A ASN* 3.3 10.4 + - - -
62A TYR* 2.5 31.1 + - - +
88A ILE* 4.4 5.5 - - - +
168A ASN* 4.1 22.4 - - - +
169A LEU* 4.6 9.1 - - + +
170A THR* 3.0 28.8 + - - +
172A GLN* 1.3 79.7 - - - +
174A LEU* 1.3 61.9 + - - +
176A TYR* 3.4 9.9 + - - -
177A SER* 3.1 20.8 + - - -
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Residues in contact with LEU 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 ILE* 4.4 9.3 - - + +
146A GLN* 4.7 14.7 - - + +
147A LEU* 4.7 12.1 - - + -
150A LEU* 4.3 24.2 - - + -
169A LEU* 4.9 9.9 - - + +
170A THR 2.7 15.4 + - - +
171A MET* 3.3 14.6 - - - +
172A GLN 3.1 0.2 - - - -
173A GLU* 1.3 74.7 - - - +
175A GLY* 1.3 61.3 + - - +
177A SER* 3.3 7.0 + - - -
178A SER* 3.0 23.3 + - - -
186A VAL* 4.0 9.0 - - + -
190A ILE* 3.8 21.3 - - + -
206A PHE* 3.6 36.1 - - + -
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Residues in contact with GLY 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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171A MET 2.9 7.7 + - - -
172A GLN* 2.9 8.2 + - - -
174A LEU* 1.3 73.7 - - - +
176A TYR* 1.3 64.5 + - - +
178A SER* 2.8 30.4 + - - +
180A ILE* 2.8 23.1 - - - +
186A VAL* 3.5 21.7 - - - +
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Residues in contact with TYR 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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47A LYS* 5.1 1.6 - - - -
57A ILE* 3.3 53.0 - - + +
58A MET* 3.5 7.8 - - - +
59A ASN* 3.0 38.7 + - - +
172A GLN* 2.8 57.3 + - + +
173A GLU* 3.4 18.8 - - - +
175A GLY* 1.3 71.6 - - - +
177A SER* 1.3 58.0 + - - +
178A SER 3.1 12.5 - - - +
180A ILE 4.1 4.5 - - - -
181A ALA* 4.8 7.9 - - - -
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Residues in contact with SER 177 (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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59A ASN* 3.4 36.4 + - - +
60A LEU 5.9 0.2 - - - -
61A GLN* 5.8 1.7 + - - -
62A TYR* 4.7 12.6 - - - -
130A LYS* 5.4 0.2 + - - -
134A PHE* 4.1 8.0 - - - -
146A GLN* 2.7 48.5 + - - +
173A GLU 3.1 9.8 + - - -
174A LEU* 3.9 7.6 - - - -
175A GLY 3.2 0.2 - - - -
176A TYR* 1.3 75.1 - - - +
178A SER* 1.3 65.1 + - - +
131B PHE* 4.4 4.9 - - - -
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Residues in contact with SER 178 (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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58A MET* 3.3 14.6 - - - +
134A PHE* 4.2 12.1 - - - -
142A SER* 4.1 19.1 - - - -
143A ILE* 3.5 18.6 - - - +
146A GLN* 4.5 3.1 - - - +
174A LEU 3.0 11.3 + - - -
175A GLY* 2.8 20.3 + - - +
176A TYR 3.1 11.1 - - - +
177A SER* 1.3 82.2 - - - +
179A GLY* 1.3 65.5 + - - -
180A ILE* 3.2 19.0 + - - +
135B SER* 5.1 0.9 - - - -
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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