Contacts of the helix formed by residues 163 - 173 (chain A) in PDB entry 1I43
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 TYR 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MET* 3.8 11.0 - - - -
161A ASP 4.4 0.4 - - - -
162A CYS* 1.3 75.9 - - - +
164A ARG* 1.3 71.5 + - + +
165A LYS* 3.4 22.8 - - + +
166A THR* 3.0 33.4 + - - +
167A ARG* 2.9 18.0 + - - +
207A GLU* 3.1 18.6 + - - +
211A ASN* 4.2 19.3 - - - +
500A PLP 3.5 37.0 - + + +
600A PMC 3.2 71.3 + + - -
110C ARG* 3.3 11.5 + - - -
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Residues in contact with ARG 164 (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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162A CYS 3.2 6.3 + - - -
163A TYR* 1.3 75.3 - - + +
165A LYS* 1.3 64.9 + - - +
167A ARG* 2.8 29.0 + - + +
168A ILE* 3.0 34.0 + - + +
211A ASN* 5.5 1.6 - - - +
403A SER* 3.0 23.4 + - - +
404A TYR* 3.4 44.4 + - + +
406A ASP* 3.0 39.6 + - - -
407A LEU* 3.7 19.6 - - - +
600A PMC 5.4 7.6 - - - +
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Residues in contact with LYS 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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139A MET* 4.0 11.0 - - - +
163A TYR* 3.4 20.8 - - + +
164A ARG* 1.3 85.7 - - - +
166A THR* 1.3 62.5 + - - +
168A ILE* 3.2 25.7 + - + +
169A PHE* 3.1 20.8 + - - +
600A PMC 4.3 14.8 + - - +
110C ARG* 4.2 12.1 - - - +
111C TYR* 3.2 34.3 + - - +
289C HIS* 4.6 6.7 + - - +
290C ILE* 4.5 26.0 - - + +
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Residues in contact with THR 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 MET* 3.8 18.1 - - + +
142A SER* 4.7 10.8 + - - -
146A LEU* 4.7 10.1 - - + -
162A CYS* 4.1 6.3 - - - -
163A TYR* 3.0 28.2 + - - +
165A LYS* 1.3 74.7 - - - +
167A ARG* 1.3 65.1 + - - +
169A PHE* 3.3 4.9 + - + +
170A ILE* 3.0 43.0 + - + +
205A PHE* 3.9 30.6 - - + -
500A PLP 4.7 2.4 - - - -
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Residues in contact with ARG 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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158A THR* 5.9 1.1 - - - -
159A THR 5.2 1.6 - - - -
160A THR* 3.6 18.4 + - - +
162A CYS* 4.5 20.6 + - + +
163A TYR 2.9 10.6 + - - +
164A ARG* 2.8 18.7 + - + +
166A THR* 1.3 77.1 - - - +
168A ILE* 1.3 61.8 + - + +
170A ILE* 3.1 11.0 + - - +
171A GLU* 2.9 59.2 + - - +
183A VAL* 4.2 25.4 - - - +
415A TYR* 2.8 51.9 + - - -
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Residues in contact with ILE 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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164A ARG* 3.0 36.4 + - + +
165A LYS* 3.2 33.8 + - - +
167A ARG* 1.3 78.1 - - + +
169A PHE* 1.3 53.6 + - - +
171A GLU* 4.7 3.6 - - - -
172A THR* 2.6 59.5 + - + +
290C ILE* 4.0 21.1 - - + -
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Residues in contact with PHE 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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139A MET* 5.2 2.2 - - + -
143A THR* 3.7 30.1 - - + +
146A LEU* 3.6 37.0 - - + -
147A LEU* 3.7 28.5 - - + -
165A LYS 3.1 12.7 + - - +
166A THR* 3.6 11.2 - - + +
167A ARG 3.3 0.2 - - - -
168A ILE* 1.3 76.3 - - - +
170A ILE* 1.3 58.9 + - + +
173A ILE* 3.1 51.7 + - + +
174A LEU* 3.2 30.9 + - + -
290C ILE* 4.0 18.8 - - + +
291C LEU* 3.8 15.7 - - + -
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Residues in contact with ILE 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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146A LEU* 4.2 15.7 - - + -
156A ILE* 4.1 9.2 - - + -
158A THR* 4.4 25.4 - - + +
162A CYS* 4.7 5.6 - - - -
166A THR* 3.0 31.6 - - + +
167A ARG* 3.1 8.4 + - - +
169A PHE* 1.3 78.5 - - + +
171A GLU* 1.3 62.2 + - + +
172A THR 3.5 0.2 - - - -
174A LEU* 3.6 29.5 - - + +
175A PRO* 3.4 16.6 - - - +
179A ILE* 4.9 3.3 - - + +
181A ALA* 4.0 28.0 - - + +
205A PHE* 4.9 3.1 - - + -
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Residues in contact with GLU 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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167A ARG* 2.9 59.7 + - + +
168A ILE* 4.2 3.6 - - - +
170A ILE* 1.3 81.2 - - + +
172A THR* 1.3 66.7 + - + +
175A PRO* 3.8 11.5 - - - +
181A ALA* 6.5 1.1 - - + -
183A VAL* 4.9 6.7 - - + +
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Residues in contact with THR 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 ILE* 2.6 40.2 + - + +
170A ILE 3.5 0.4 - - - -
171A GLU* 1.3 89.0 - - + +
173A ILE* 1.3 79.0 + - - +
175A PRO* 3.6 9.6 - - - +
176A LYS* 3.7 20.1 - - - +
290C ILE* 5.4 0.3 - - - +
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Residues in contact with ILE 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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147A LEU* 5.5 7.2 - - + -
169A PHE* 3.1 44.9 + - + +
172A THR* 1.3 94.6 - - - +
174A LEU* 1.3 66.7 + - - +
175A PRO* 3.2 2.2 - - - -
176A LYS* 3.0 41.9 + - + +
177A MET* 4.0 5.3 + - + +
147C LEU* 6.0 8.7 - - + +
177C MET* 5.3 6.9 - - + +
287C LEU* 3.8 29.6 - - + -
290C ILE* 5.5 5.4 - - + -
291C LEU* 5.9 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