Contacts of the helix formed by residues 168 - 177 (chain I) in PDB entry 5XS0
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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H HIS* 3.6 29.9 + - + +
70H ARG* 3.9 9.1 + - - -
186H VAL* 4.3 2.6 - - - +
46I ARG* 4.0 19.0 + - - +
164I ASN 4.4 0.4 + - - -
165I CYS* 2.8 17.4 + - + +
167I LEU* 1.3 75.8 - - - +
169I LYS* 1.3 69.3 + - - +
170I ASP* 3.3 24.3 + - - +
171I TYR* 3.1 19.1 + - + +
172I LEU* 3.0 24.7 + - - +
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Residues in contact with LYS 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H TYR* 5.0 7.9 + - - -
67H GLU* 4.0 27.4 + - - +
69H HIS* 5.2 0.8 - - - -
167I LEU 3.5 8.0 + - - +
168I ASP* 1.3 75.5 + - - +
170I ASP* 1.3 62.2 + - - +
172I LEU* 3.2 15.8 + - + +
173I ARG* 2.9 34.5 + - + +
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Residues in contact with ASP 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H ARG* 4.0 12.9 + - - -
183H PRO* 3.5 14.0 - - - +
184H LEU* 3.5 32.0 + - - +
186H VAL* 3.6 13.9 - - + -
168I ASP* 3.2 14.9 - - - +
169I LYS* 1.3 78.9 - - - +
171I TYR* 1.3 60.0 + - - +
173I ARG* 3.0 27.0 + - - +
174I SER* 2.9 32.6 + - - -
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Residues in contact with TYR 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H VAL* 3.7 10.9 - - - +
188H LEU* 3.5 38.1 - - + -
46I ARG* 3.7 19.3 - - + +
47I LEU* 2.4 40.0 + - - +
52I ILE* 3.8 5.2 - - + +
165I CYS* 3.0 46.9 - - + +
166I ILE* 3.8 16.6 - - + -
168I ASP* 3.1 20.5 + - + +
170I ASP* 1.3 77.1 - - - +
172I LEU* 1.3 61.4 + - + +
174I SER* 3.4 2.1 + - - -
175I LEU* 2.9 48.8 + - + +
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Residues in contact with LEU 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I CYS* 3.8 32.3 - - + -
166I ILE* 3.9 35.2 - - + +
167I LEU 5.6 0.9 - - - -
168I ASP 3.0 17.4 + - - +
169I LYS* 3.5 17.5 - - + +
170I ASP 3.2 0.6 - - - -
171I TYR* 1.3 80.0 - - + +
173I ARG* 1.3 65.4 + - - +
175I LEU* 3.0 13.0 + - + +
176I ASN* 3.0 28.9 + - - +
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Residues in contact with ARG 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H PRO* 3.6 18.8 + - - +
184H LEU 3.4 18.2 + - - -
185H GLU* 4.8 8.3 - - - +
169I LYS* 2.9 18.3 + - + +
170I ASP* 3.0 34.3 + - - +
172I LEU* 1.3 76.8 - - + +
174I SER* 1.3 62.0 + - - +
176I ASN* 3.1 17.4 + - - +
177I LYS* 3.3 38.6 + - - +
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Residues in contact with SER 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185H GLU* 4.0 8.5 - - - +
186H VAL* 2.8 48.1 + - - -
188H LEU* 3.4 19.3 - - - +
170I ASP 2.9 14.1 + - - -
171I TYR 3.7 5.2 - - - -
173I ARG* 1.3 77.3 + - - +
175I LEU* 1.3 60.2 + - - +
177I LYS* 4.1 15.2 + - - +
178I LEU* 3.9 12.6 + - - +
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Residues in contact with LEU 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H LEU* 3.7 14.6 - - + -
47I LEU 4.4 0.7 - - - +
49I PRO* 3.9 41.7 - - + +
52I ILE* 3.6 28.3 - - + -
64I CYS* 5.9 0.7 - - - -
171I TYR* 2.9 48.7 + - + +
172I LEU* 3.0 18.8 + - + +
174I SER* 1.3 77.0 - - - +
176I ASN* 1.3 64.2 + - - +
178I LEU* 3.3 20.0 + - + +
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Residues in contact with ASN 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I LYS* 3.9 27.5 + - - +
172I LEU* 3.0 16.6 + - - +
173I ARG* 3.1 10.4 + - - +
175I LEU* 1.3 79.2 - - - +
177I LYS* 1.3 61.3 + - + +
178I LEU 3.1 9.8 + - - +
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Residues in contact with LYS 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185H GLU* 2.3 39.4 + - + +
173I ARG* 3.3 31.9 + - - +
174I SER* 4.4 12.3 - - - +
175I LEU 3.3 0.8 - - - -
176I ASN* 1.3 76.9 - - + +
178I LEU* 1.3 62.4 + - + +
179I PRO* 4.0 2.9 - - - +
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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