Contacts of the helix formed by residues 168 - 177 (chain N) in PDB entry 1H2I
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 ASP 168 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M GLU* 5.3 0.2 - - - +
69M HIS* 3.4 38.0 + - + +
70M ARG* 4.2 5.7 + - - -
186M VAL* 4.6 2.9 - - - +
46N ARG* 3.0 28.5 + - - +
165N CYS* 2.7 22.4 + - - +
166N ILE 3.5 0.4 - - - -
167N LEU* 1.3 70.5 - - - +
169N LYS* 1.3 59.3 + - - +
170N ASP* 3.2 21.3 + - - +
171N TYR* 2.8 32.4 + - + +
172N LEU* 3.0 11.8 + - - +
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Residues in contact with LYS 169 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M TYR* 5.4 4.2 + - - -
67M GLU* 4.3 21.9 + - - +
69M HIS* 5.0 1.2 - - - -
167N LEU 3.3 9.7 + - - +
168N ASP* 1.3 74.2 + - - +
170N ASP* 1.3 59.9 + - - +
171N TYR 3.2 0.2 - - - -
172N LEU* 3.7 14.2 - - + +
173N ARG* 3.0 30.3 + - - +
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Residues in contact with ASP 170 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70M ARG* 3.8 20.8 + - - -
183M PRO* 3.6 11.8 - - - +
184M LEU* 3.4 27.3 + - + +
186M VAL* 3.3 25.4 + - + +
168N ASP* 3.0 7.7 + - - +
169N LYS* 1.3 77.3 - - - +
171N TYR* 1.3 64.7 + - - +
173N ARG* 2.7 32.5 + - - +
174N SER* 3.1 20.1 + - - -
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Residues in contact with TYR 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186M VAL* 3.6 10.2 - - + +
188M LEU* 3.9 14.1 - - + -
46N ARG* 3.7 38.6 - - + +
47N LEU 2.5 31.3 + - - -
52N ILE* 3.5 24.8 - - + +
165N CYS* 3.7 31.8 - - + +
166N ILE* 4.2 9.2 - - - -
168N ASP* 2.8 24.8 + - + +
170N ASP* 1.3 77.5 - - - +
172N LEU* 1.3 78.8 + - + +
174N SER* 3.3 3.6 + - - -
175N LEU* 3.0 43.8 + - + +
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Residues in contact with LEU 172 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64N CYS* 3.8 35.9 - - + +
166N ILE* 3.6 27.1 - - + +
167N LEU* 4.6 6.1 - - - +
168N ASP 3.0 16.4 + - - +
169N LYS* 3.7 18.6 - - + +
171N TYR* 1.3 93.0 - - + +
173N ARG* 1.3 62.0 + - - +
175N LEU* 3.0 20.2 + - + +
176N ASN* 3.0 23.1 + - - +
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Residues in contact with ARG 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183M PRO* 3.5 12.9 - - - +
184M LEU 2.9 19.8 + - - -
185M GLU* 2.8 26.4 + - - +
169N LYS* 3.0 16.5 + - - +
170N ASP* 2.7 37.9 + - - +
172N LEU* 1.3 77.2 - - - +
174N SER* 1.3 63.6 + - - +
176N ASN* 3.2 22.4 + - - +
177N LYS* 3.5 32.3 + - - +
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Residues in contact with SER 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M GLU* 5.9 3.8 - - - -
186M VAL* 3.1 29.8 + - - +
188M LEU* 3.0 26.2 - - - +
170N ASP 3.1 14.9 + - - -
171N TYR 3.9 1.5 + - - -
173N ARG* 1.3 81.1 - - - +
175N LEU* 1.3 62.4 + - - +
176N ASN 3.3 0.2 - - - -
177N LYS* 3.7 21.8 + - - +
178N LEU* 3.9 9.9 - - - +
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Residues in contact with LEU 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M LEU* 3.9 14.6 - - + -
47N LEU 4.6 0.7 - - - +
48N GLY* 4.5 1.1 - - - -
49N PRO* 3.9 38.8 - - + +
52N ILE* 3.7 35.0 - - + -
64N CYS* 5.5 2.5 - - - -
171N TYR* 3.0 38.2 + - + +
172N LEU* 3.0 17.2 + - + +
174N SER* 1.3 74.8 - - - +
176N ASN* 1.3 61.4 + - - +
177N LYS 3.2 0.4 - - - -
178N LEU* 3.0 29.4 + - + +
179N PRO 5.1 0.5 - - - +
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Residues in contact with ASN 176 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N LYS* 3.8 28.3 + - - +
64N CYS* 5.8 3.8 - - - -
172N LEU* 3.0 22.0 + - - +
173N ARG* 3.4 12.2 - - - +
175N LEU* 1.3 73.5 - - - +
177N LYS* 1.3 58.0 + - + +
178N LEU 2.9 18.3 + - - +
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Residues in contact with LYS 177 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M GLU* 3.3 24.6 + - - +
173N ARG* 3.5 37.3 + - - +
174N SER* 3.9 15.8 - - - +
175N LEU 3.2 1.0 - - - -
176N ASN* 1.3 76.3 - - + +
178N LEU* 1.3 64.7 + - - +
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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