Contacts of the helix formed by residues 173 - 183 (chain A) in PDB entry 4A8X
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 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ASN 3.9 10.1 - - - +
172A VAL* 1.3 76.1 - - - +
174A LYS* 1.3 65.5 + - - +
175A ASP* 3.5 10.2 + - - +
176A HIS* 3.0 48.0 + - + +
177A ILE* 3.2 13.9 + - - +
192A MET* 3.8 3.6 - - - -
666B GLY 5.8 0.3 - - - -
667B THR 4.2 13.4 + - - +
668B PRO* 4.7 4.7 - - + -
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Residues in contact with LYS 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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173A THR* 1.3 73.0 - - - +
175A ASP* 1.3 59.3 + - - +
177A ILE* 3.2 5.6 + - - +
178A MET* 3.0 25.3 + - - +
190A ILE* 4.5 10.2 - - + +
192A MET* 3.6 30.9 - - + +
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Residues in contact with ASP 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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173A THR* 3.2 9.4 + - - +
174A LYS* 1.3 77.4 - - - +
176A HIS* 1.3 59.9 + - - +
178A MET* 3.3 10.8 + - - +
179A GLU* 2.9 31.4 + - - +
666B GLY* 5.5 10.3 - - - -
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Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASN 3.6 16.8 - - - -
172A VAL* 3.6 9.7 - - + -
173A THR* 3.0 43.0 + - + +
175A ASP* 1.3 75.7 - - - +
177A ILE* 1.3 57.5 + - - +
179A GLU* 3.3 5.1 + - - +
180A ILE* 2.9 39.2 + - + +
664B THR* 3.4 26.2 + - + -
666B GLY* 3.1 19.7 + - - -
667B THR 4.1 3.1 - - - -
668B PRO* 2.8 30.6 + - + -
670B ILE* 3.5 25.4 - - + +
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Residues in contact with ILE 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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165A ILE* 4.7 2.7 - - + -
168A LEU* 3.7 30.7 - - + -
172A VAL* 3.8 13.5 - - + -
173A THR 3.2 12.3 + - - +
174A LYS* 3.5 9.6 - - - +
175A ASP 3.2 0.2 - - - -
176A HIS* 1.3 79.6 - - - +
178A MET* 1.3 65.3 + - - +
180A ILE* 4.7 0.7 - - + -
181A PHE* 3.0 46.6 + - + +
187A ILE* 4.4 0.3 - - - +
190A ILE* 4.2 12.3 - - + -
192A MET* 3.9 17.9 - - - -
206A ALA* 4.5 4.5 - - + -
208A VAL* 3.6 29.8 - - + -
228A ILE* 4.3 5.4 - - + -
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Residues in contact with MET 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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174A LYS 3.0 13.4 + - - +
175A ASP* 3.6 15.5 - - - +
176A HIS 3.3 0.2 - - - -
177A ILE* 1.3 78.2 - - - +
179A GLU* 1.3 62.1 + - - +
182A SER* 2.7 51.0 + - - +
186A LYS* 5.9 6.7 - - + +
187A ILE* 3.9 29.8 - - + +
190A ILE* 3.9 17.7 - - + +
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Residues in contact with GLU 179 (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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175A ASP 2.9 17.5 + - - +
176A HIS* 3.7 4.8 - - - +
178A MET* 1.3 80.7 - - - +
180A ILE* 1.3 64.2 + - + +
182A SER* 3.7 9.0 + - - -
183A THR* 3.8 9.9 + - - -
663B LYS 4.3 2.3 - - - +
664B THR* 3.3 19.3 - - + -
665B LYS* 2.9 31.9 + - - +
666B GLY* 3.0 27.0 + - - -
672B TRP* 5.4 2.4 + - - +
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Residues in contact with ILE 180 (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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176A HIS* 2.9 28.7 + - + +
177A ILE* 5.0 1.3 - - + +
178A MET 3.4 0.2 - - - -
179A GLU* 1.3 74.6 - - + +
181A PHE* 1.3 82.7 + - + +
183A THR* 2.7 29.3 + - - -
184A TYR* 3.9 4.1 - - + -
223A MET* 4.1 8.3 - - + -
228A ILE* 3.8 32.5 - - + -
664B THR* 4.2 14.4 - - + -
670B ILE* 4.5 2.5 - - + -
672B TRP* 3.7 57.4 - - + +
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Residues in contact with PHE 181 (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* 5.4 0.7 - - + -
165A ILE* 3.6 37.0 - - + -
177A ILE* 3.0 37.5 + - + +
180A ILE* 1.3 79.3 - - + +
182A SER* 1.3 59.8 + - - +
183A THR 3.0 2.2 - - - -
184A TYR* 2.9 26.5 + + - +
187A ILE* 3.9 15.0 - - + -
208A VAL* 4.5 8.1 - - + -
210A PHE* 3.4 24.6 - + + -
219A ALA* 4.2 23.8 - - + -
223A MET* 3.9 25.6 - - + -
228A ILE* 3.8 22.4 - - + -
233A ILE* 4.0 18.2 - - + -
235A ALA* 5.4 0.2 - - + -
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Residues in contact with SER 182 (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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178A MET* 2.7 44.8 + - - +
179A GLU* 3.9 6.7 - - - -
180A ILE 3.3 0.2 - - - -
181A PHE* 1.3 72.7 - - - +
183A THR* 1.3 65.5 + - - +
184A TYR 3.0 3.1 + - - -
185A GLY 3.2 22.6 + - - +
187A ILE* 3.7 10.0 + - - +
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Residues in contact with THR 183 (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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179A GLU 3.8 6.2 + - - -
180A ILE 2.7 22.3 + - - -
182A SER* 1.3 79.8 - - - +
184A TYR* 1.3 83.2 + - + +
185A GLY 4.0 0.2 + - - -
218A LYS* 4.6 8.5 + - - -
662B ARG* 4.0 19.3 - - - +
672B TRP* 3.6 14.0 - - + -
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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