Contacts of the helix formed by residues 188 - 202 (chain K) in PDB entry 1IA0
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 SER 188 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127K PHE* 3.4 20.3 - - - -
131K ASN* 5.8 2.0 - - - +
186K VAL* 4.5 0.5 - - - +
187K THR* 1.3 80.5 + - - +
189K TYR* 1.3 64.8 + - - +
190K ASN* 3.6 10.1 + - - +
191K ASP* 3.0 35.6 + - - +
192K ILE* 3.2 15.4 + - - +
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Residues in contact with TYR 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K GLN* 4.9 1.0 + - - +
116K GLN* 5.2 7.1 + - - +
120K PRO* 3.6 30.3 + - - +
123K CYS* 3.9 7.2 - - + -
124K GLU* 3.6 42.9 - - + +
127K PHE* 3.6 27.3 - - + +
188K SER* 1.3 70.4 - - - +
190K ASN* 1.3 72.6 + - - +
192K ILE* 3.1 12.5 - - + +
193K GLN* 2.6 67.5 + - + +
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Residues in contact with ASN 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K SER* 3.3 9.5 + - - +
189K TYR* 1.3 88.2 - - - +
191K ASP* 1.3 60.1 + - - +
193K GLN* 3.3 6.8 + - - +
194K ASP* 3.0 35.9 + - - +
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Residues in contact with ASP 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K VAL* 4.6 14.1 - - + -
187K THR* 4.2 13.4 + - - +
188K SER* 3.0 28.0 + - - +
190K ASN* 1.3 77.8 - - - +
192K ILE* 1.3 65.8 + - - +
194K ASP* 3.2 13.3 + - - +
195K LEU* 3.2 26.5 + - + +
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Residues in contact with ILE 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K CYS* 3.9 27.8 - - + -
126K LEU* 5.7 0.2 - - + -
127K PHE* 3.9 18.2 - - + -
142K VAL* 4.5 4.3 - - + -
144K VAL* 4.5 13.9 - - + -
186K VAL* 4.0 24.8 - - + +
188K SER 3.2 8.0 + - - +
189K TYR* 3.1 35.5 + - + +
191K ASP* 1.3 77.4 - - - +
193K GLN* 1.3 69.5 + - - +
195K LEU* 3.2 5.6 + - + +
196K MET* 2.9 23.6 + - + +
221K PHE* 4.4 15.3 - - + -
223K ILE* 4.3 14.8 - - + -
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Residues in contact with GLN 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K MET* 5.5 0.8 - - - -
111K GLN* 2.9 30.7 + - - +
120K PRO* 4.0 8.7 - - - +
189K TYR* 2.6 55.6 + - + +
190K ASN* 3.5 7.9 - - - +
192K ILE* 1.3 79.5 - - - +
194K ASP* 1.3 58.7 + - - +
196K MET* 3.1 30.5 + - - +
197K ASP* 2.8 56.5 + - - +
200K ASN* 5.7 0.4 - - - +
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Residues in contact with ASP 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K ASN* 3.0 22.8 + - - +
191K ASP* 3.2 15.9 + - - +
193K GLN* 1.3 80.5 - - - +
195K LEU* 1.3 62.2 + - + +
197K ASP* 3.4 12.3 + - - +
198K SER* 3.1 24.3 + - - -
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Residues in contact with LEU 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144K VAL* 3.8 18.8 - - + -
158K LEU* 3.7 25.8 - - + +
184K LEU* 3.8 28.9 - - + -
186K VAL* 3.4 32.8 - - + -
191K ASP* 3.2 11.8 + - + +
192K ILE* 3.5 7.0 - - - +
194K ASP* 1.3 75.1 - - + +
196K MET* 1.3 61.2 + - - +
198K SER* 3.1 9.2 + - - +
199K GLY* 2.9 27.5 + - - -
221K PHE* 5.8 1.1 - - + -
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Residues in contact with MET 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K MET* 3.5 39.3 - - + +
119K ILE* 3.7 24.9 - - + -
120K PRO* 4.0 9.0 - - + -
123K CYS* 3.7 22.0 - - + -
146K TYR* 3.9 9.7 - - + -
192K ILE* 2.9 12.4 + - + +
193K GLN* 3.1 38.3 + - - +
195K LEU* 1.3 76.8 - - - +
197K ASP* 1.3 56.5 + - - +
199K GLY* 3.3 1.0 + - - -
200K ASN* 2.8 37.2 + - - +
221K PHE* 3.9 19.0 - - + -
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Residues in contact with ASP 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K GLN* 3.6 24.1 + - - +
193K GLN* 2.8 44.9 + - - +
194K ASP* 3.6 13.6 - - - +
196K MET* 1.3 73.8 - - - +
198K SER* 1.3 65.5 + - - +
200K ASN* 3.3 12.8 + - - +
201K LYS* 3.1 30.5 + - - +
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Residues in contact with SER 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K LEU 4.4 4.1 + - - +
158K LEU* 5.0 2.6 - - - +
160K PRO* 5.7 1.2 - - - +
194K ASP 3.1 10.4 + - - -
195K LEU* 3.1 18.9 + - - +
197K ASP* 1.3 78.4 - - - +
199K GLY* 1.3 65.3 + - - +
201K LYS* 3.1 31.5 + - - +
202K ALA* 3.2 13.9 + - - +
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Residues in contact with GLY 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K TYR* 3.9 18.8 - - - -
157K LEU* 3.5 29.1 - - - +
195K LEU 2.9 18.2 + - - -
196K MET 3.6 1.3 - - - -
198K SER* 1.3 77.3 + - - +
200K ASN* 1.3 57.7 + - - +
202K ALA* 2.8 23.4 + - - +
203K ARG 3.6 4.2 + - - -
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Residues in contact with ASN 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K MET* 3.2 37.2 - - - +
146K TYR* 2.6 30.0 + - - -
193K GLN* 5.7 0.4 - - - +
196K MET* 2.8 23.0 + - - +
197K ASP* 3.3 12.8 + - - +
199K GLY* 1.3 74.6 - - - +
201K LYS* 1.3 60.0 + - + +
202K ALA 3.5 0.5 + - - -
203K ARG* 3.8 24.2 + - - +
213K THR* 5.2 3.3 + - - -
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Residues in contact with LYS 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197K ASP* 3.1 18.4 + - - +
198K SER* 3.1 26.6 + - - +
199K GLY 3.0 1.0 - - - -
200K ASN* 1.3 79.6 - - + +
202K ALA* 1.3 56.0 + - - +
203K ARG 3.5 3.4 + - - +
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Residues in contact with ALA 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155K ARG* 3.0 24.9 + - - +
157K LEU* 3.5 20.8 - - + +
160K PRO* 4.0 28.9 - - + -
198K SER 3.2 8.4 + - - +
199K GLY 2.8 9.8 + - - +
201K LYS* 1.3 79.3 - - - +
203K ARG* 1.3 62.3 + - - +
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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