Contacts of the helix formed by residues 180 - 192 (chain H) in PDB entry 3IYD
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 ARG 180 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57H LYS* 3.5 29.1 - - - +
169H ARG* 4.4 15.0 - - + +
170H GLN* 3.8 27.5 - - + +
173H GLY* 6.0 0.4 - - - -
179H SER* 1.3 72.4 - - - +
181H GLU* 1.3 92.2 + - - +
183H VAL* 3.6 4.2 + - - +
184H GLY* 3.5 15.9 + - - -
10I T 3.6 40.6 + - - +
11I G 3.6 27.7 + - - +
86J C 4.8 12.9 + - - +
87J A 4.2 13.3 + - - +
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Residues in contact with GLU 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179H SER* 3.3 20.7 - - - +
180H ARG* 1.3 114.0 + - + +
182H THR* 1.3 65.3 + - - +
184H GLY* 3.4 3.7 + - - -
185H ARG* 3.2 41.1 + - - +
11I G 4.5 4.7 - - - +
12I T 3.9 30.1 - - + +
13I G 4.0 11.4 - - - +
84J A 6.0 1.1 - - - +
85J T 4.2 17.9 - - + +
86J C 4.3 11.9 + - - +
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Residues in contact with THR 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H VAL* 4.2 26.0 - - + -
178H CYS* 4.9 3.8 - - - -
179H SER* 2.9 23.7 + - - -
180H ARG 3.4 0.2 - - - -
181H GLU* 1.3 78.6 - - - +
183H VAL* 1.3 62.4 + - - +
185H ARG* 3.3 12.9 + - - +
186H ILE* 3.2 39.8 + - + +
83J G 5.2 10.9 + - + +
84J A 3.6 22.4 + - - +
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Residues in contact with VAL 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H ILE* 5.0 15.2 - - + +
169H ARG* 3.5 41.5 - - + +
172H ILE* 4.1 24.0 - - + -
173H GLY* 3.9 11.2 - - - +
178H CYS* 3.6 19.3 - - - -
179H SER 3.3 18.6 - - - +
180H ARG 3.6 4.2 + - - +
181H GLU 3.3 0.6 - - - -
182H THR* 1.3 77.9 - - - +
184H GLY* 1.3 56.6 + - - +
186H ILE* 4.1 1.3 - - - +
187H LEU* 3.0 34.8 + - + +
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Residues in contact with GLY 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H ARG* 3.8 23.3 - - - +
180H ARG 3.5 6.8 + - - -
181H GLU* 3.4 6.1 + - - -
182H THR 3.3 0.6 - - - -
183H VAL* 1.3 78.4 - - - +
185H ARG* 1.3 61.5 + - - +
187H LEU* 3.8 1.6 - - - +
188H LYS* 3.2 34.4 + - - +
11I G 4.4 9.9 - - - -
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Residues in contact with ARG 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H GLU* 3.2 27.0 + - - +
182H THR* 3.6 14.3 + - - +
183H VAL 3.3 0.6 - - - -
184H GLY* 1.3 79.3 - - - +
186H ILE* 1.3 69.8 + - + +
188H LYS* 3.4 4.7 + - - +
189H MET* 3.2 25.4 + - + +
12I T 5.5 8.2 + - + +
13I G 4.2 30.1 + - - -
14I A 4.7 6.7 - - - +
83J G 4.5 9.7 + - - -
84J A 3.9 24.7 - - - +
85J T 5.3 1.4 + - - -
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Residues in contact with ILE 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H VAL* 4.4 16.2 - - + -
140H THR* 5.5 12.3 - - + +
143H ILE* 4.7 17.5 - - + -
182H THR* 3.2 35.3 + - + +
183H VAL 4.3 1.8 - - - +
185H ARG* 1.3 81.1 - - + +
187H LEU* 1.3 67.3 + - - +
189H MET* 3.0 31.1 + - + +
190H LEU* 3.1 32.3 + - + +
83J G 6.2 0.4 - - - +
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Residues in contact with LEU 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H ARG* 3.7 44.0 - - + +
172H ILE* 5.5 3.8 - - + -
183H VAL* 3.0 21.9 + - + +
184H GLY 3.8 4.3 - - - +
186H ILE* 1.3 82.2 - - - +
188H LYS* 1.3 63.3 + - + +
190H LEU* 3.6 9.1 + - + +
191H GLU* 3.2 24.5 + - - +
196H ILE* 3.6 24.6 - - + +
198H ALA* 4.2 17.5 - - + -
203H ILE* 4.3 24.5 - - + -
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Residues in contact with LYS 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H ARG* 5.4 4.9 - - - +
184H GLY* 3.2 18.5 + - - +
185H ARG* 3.9 4.5 - - - +
186H ILE 3.2 0.6 - - - -
187H LEU* 1.3 77.7 - - + +
189H MET* 1.3 64.6 + - - +
191H GLU* 3.3 34.1 + - - +
192H ASP* 3.6 14.1 - - - +
11I G 3.6 47.4 + - - -
12I T 4.6 7.3 + - - -
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Residues in contact with MET 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H ARG* 3.2 17.3 + - + +
186H ILE* 3.0 27.5 + - + +
188H LYS* 1.3 79.9 - - - +
190H LEU* 1.3 65.6 + - + +
191H GLU 3.3 0.3 + - - -
192H ASP* 3.4 16.3 + - - +
193H GLN* 3.7 28.5 + - - +
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Residues in contact with LEU 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H THR* 6.3 3.4 - - + -
143H ILE* 6.0 5.4 - - + -
147H LEU* 5.8 6.3 - - + -
186H ILE* 3.1 30.2 + - + +
187H LEU* 3.6 1.5 + - - +
189H MET* 1.3 81.2 - - + +
191H GLU* 1.3 61.5 + - - +
193H GLN* 3.5 11.4 + - - +
194H ASN 3.5 3.5 + - - -
195H LEU* 3.2 53.4 + - + +
196H ILE* 3.8 36.6 + - + -
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Residues in contact with GLU 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H LEU* 3.2 22.4 - - - +
188H LYS* 3.4 24.8 - - - +
189H MET 3.1 0.4 - - - -
190H LEU* 1.3 78.1 - - - +
192H ASP* 1.3 67.0 + - - +
194H ASN* 3.3 12.1 + - - -
196H ILE* 4.4 21.8 - - + +
197H SER* 4.9 0.9 - - - -
198H ALA* 3.4 38.4 - - + +
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Residues in contact with ASP 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H LYS 3.6 14.8 - - - +
189H MET* 3.4 10.9 + - - +
190H LEU 3.3 0.4 - - - -
191H GLU* 1.3 79.0 - - - +
193H GLN* 1.3 62.1 - - + +
194H ASN* 3.2 4.2 + - - +
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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