Contacts of the helix formed by residues 168 - 177 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69I HIS* 3.6 36.4 + - + +
70I ARG* 4.3 6.2 + - - -
186I VAL* 5.0 0.9 - - - +
46J ARG* 3.0 28.2 + - - -
165J CYS* 2.6 23.0 + - - +
166J ILE 3.5 0.4 - - - -
167J LEU* 1.3 69.2 - - - +
169J LYS* 1.3 58.8 + - - +
170J ASP* 3.1 23.4 + - - +
171J TYR* 2.8 32.0 + - + +
172J LEU* 3.0 12.9 + - - +
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Residues in contact with LYS 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I TYR* 5.6 2.6 + - - -
67I GLU* 4.3 20.0 + - - +
69I HIS* 5.2 0.8 - - - -
167J LEU 3.4 10.1 + - - +
168J ASP* 1.3 72.9 + - - +
170J ASP* 1.3 59.5 + - - +
172J LEU* 3.4 14.8 + - + +
173J ARG* 2.9 32.6 + - - +
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Residues in contact with ASP 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I ARG* 3.9 14.4 + - - -
183I PRO* 3.1 24.1 - - - +
184I LEU 3.8 13.3 + - - +
186I VAL* 3.3 17.2 + - + +
168J ASP* 3.0 14.3 + - - +
169J LYS* 1.3 78.7 - - - +
171J TYR* 1.3 61.1 + - - +
173J ARG* 2.8 37.3 + - - +
174J SER* 3.2 18.9 + - - -
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Residues in contact with TYR 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I VAL* 3.6 12.2 - - + +
188I LEU* 4.0 15.0 - - + -
46J ARG* 3.7 37.0 - - + +
47J LEU 2.6 30.5 + - - -
52J ILE* 3.4 25.2 - - + +
165J CYS* 3.7 33.4 - - + -
166J ILE* 4.2 9.6 - - - -
168J ASP* 2.8 25.0 + - + +
170J ASP* 1.3 77.8 - - - +
172J LEU* 1.3 76.1 + - + +
174J SER* 3.3 3.5 + - - -
175J LEU* 3.0 44.5 + - + +
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Residues in contact with LEU 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J ILE* 5.4 0.2 - - + -
64J CYS* 3.9 35.0 - - + +
166J ILE* 3.5 27.1 - - + +
167J LEU* 4.7 4.9 - - - +
168J ASP 3.0 15.9 + - - +
169J LYS* 3.7 18.6 - - + +
171J TYR* 1.3 93.0 - - + +
173J ARG* 1.3 61.8 + - - +
175J LEU* 3.0 19.6 + - + +
176J ASN* 3.1 22.8 + - - +
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Residues in contact with ARG 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183I PRO* 3.2 26.7 + - - +
184I LEU 3.6 6.1 + - - -
185I GLU* 3.0 29.4 + - - +
169J LYS* 2.9 15.5 + - - +
170J ASP* 2.8 40.0 + - - +
172J LEU* 1.3 76.5 - - - +
174J SER* 1.3 59.8 + - - +
175J LEU 3.1 4.9 + - - -
176J ASN* 3.1 22.6 + - - +
177J LYS* 3.5 26.7 + - - +
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Residues in contact with SER 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I GLU* 5.0 9.9 - - - -
186I VAL* 3.2 26.0 + - - +
188I LEU* 3.0 33.4 - - - +
170J ASP 3.2 15.1 + - - -
171J TYR 3.3 1.6 + - - -
173J ARG* 1.3 78.5 - - - +
175J LEU* 1.3 60.4 + - - +
177J LYS* 3.8 21.5 + - - +
178J LEU* 3.9 9.2 - - - +
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Residues in contact with LEU 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188I LEU* 3.8 15.0 - - + -
47J LEU 4.8 0.7 - - - +
48J GLY 4.6 0.7 - - - -
49J PRO* 3.8 40.9 - - + +
52J ILE* 3.6 35.2 - - + -
64J CYS* 5.7 1.6 - - - -
171J TYR* 3.0 37.7 + - + +
172J LEU* 3.0 17.7 + - + +
174J SER* 1.3 76.8 - - - +
176J ASN* 1.3 65.9 + - - +
177J LYS 3.2 0.4 - - - -
178J LEU* 3.3 22.6 - - + +
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Residues in contact with ASN 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J LYS* 3.6 30.0 + - - +
64J CYS* 5.9 2.6 - - - -
172J LEU* 3.1 18.8 + - - +
173J ARG* 3.4 12.4 - - - +
175J LEU* 1.3 77.7 - - - +
177J LYS* 1.3 52.3 + - + +
178J LEU 2.8 25.2 + - - +
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Residues in contact with LYS 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I GLU* 3.0 29.1 + - - +
173J ARG* 3.5 31.9 + - - +
174J SER* 4.0 15.7 - - - +
175J LEU 3.2 0.8 - - - -
176J ASN* 1.3 75.1 - - + +
178J LEU* 1.3 69.8 + - - +
179J PRO* 4.8 0.3 - - - +
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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