Contacts of the helix formed by residues 158 - 163 (chain U) 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 PHE 158 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76T ASN* 3.5 15.2 + - - +
81T TYR* 3.7 25.3 - - + +
43U LEU* 3.3 26.3 - - + +
79U PHE* 4.3 4.3 - + - -
113U VAL* 3.9 27.8 - - + -
115U LEU* 3.5 40.8 - - + -
119U SER* 4.3 6.1 - - - -
120U TYR 4.7 2.5 - - - -
121U HIS* 3.2 39.5 - + + -
154U ALA 4.4 0.9 - - - -
155U LEU* 3.7 27.1 - - + -
156U ARG 3.0 1.6 + - - -
157U SER* 1.3 79.6 - - - +
159U GLY* 1.3 55.7 + - - +
162U LEU* 3.6 22.2 - - + -
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Residues in contact with GLY 159 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73T ASN* 4.1 7.4 - - - -
76T ASN* 3.7 11.2 - - - +
43U LEU* 4.0 9.8 - - - +
155U LEU 4.6 0.2 + - - -
156U ARG 3.3 6.2 + - - +
157U SER 3.5 1.4 - - - -
158U PHE* 1.3 80.9 - - - +
160U ASN* 1.3 66.1 + - - -
161U ALA 3.3 3.1 - - - -
162U LEU* 3.3 8.9 + - - +
163U GLY 3.5 0.5 + - - -
164U ASN* 3.1 22.1 + - - +
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Residues in contact with ASN 160 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69T HIS* 6.0 0.7 - - - -
73T ASN* 3.3 32.1 + - - +
43U LEU 3.2 4.6 + - - -
44U ARG* 3.5 25.3 + - - +
45U GLN 3.5 14.1 - - - +
46U ARG* 4.2 15.3 + - + +
47U LEU* 3.1 12.5 - - - +
159U GLY* 1.3 72.3 - - - -
161U ALA* 1.3 64.5 + - - +
163U GLY 2.9 12.0 + - - -
164U ASN 3.5 0.5 + - - -
165U CYS* 3.3 44.2 + - + +
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Residues in contact with ALA 161 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192T LYS* 4.6 12.8 - - + -
42U ALA 3.5 25.6 - - - +
43U LEU* 3.0 23.1 + - + +
45U GLN 3.0 13.5 + - - +
47U LEU* 3.4 19.9 - - - +
74U LEU* 3.6 19.5 - - + +
78U MET* 4.6 7.8 - - + +
159U GLY 3.3 0.4 - - - -
160U ASN* 1.3 75.6 - - - +
162U LEU* 1.3 58.9 + - + +
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Residues in contact with LEU 162 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43U LEU* 3.9 13.5 - - + -
66U ILE* 4.9 4.0 - - - +
71U VAL* 4.3 19.2 - - + +
74U LEU* 3.8 19.3 - - + +
75U ALA* 3.7 33.4 - - + +
78U MET* 4.5 3.8 - - + -
79U PHE* 3.5 30.3 - - + -
152U LYS 4.8 0.5 - - - +
155U LEU* 3.4 26.2 - - + +
156U ARG* 3.9 14.5 + - - +
158U PHE* 3.6 27.6 - - + -
159U GLY 3.3 7.2 + - - +
160U ASN 3.1 1.0 - - - -
161U ALA* 1.3 78.2 - - - +
163U GLY* 1.3 56.9 + - - +
164U ASN 3.8 0.7 - - - -
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Residues in contact with GLY 163 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47U LEU* 4.6 0.7 - - - -
66U ILE* 3.7 23.8 - - - -
156U ARG* 3.4 17.7 - - - +
160U ASN 2.9 7.5 + - - -
161U ALA 3.4 1.2 + - - -
162U LEU* 1.3 80.9 - - - +
164U ASN* 1.3 65.2 + - - +
165U CYS 3.3 2.2 - - - -
166U ILE* 3.1 24.7 - - - +
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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