Contacts of the helix formed by residues 185 - 190 (chain A) in PDB entry 1XBT
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 CYS 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A CYS* 3.4 8.6 - - + +
156A CYS* 3.9 0.7 - - - -
159A GLU 3.4 23.8 - - - +
160A ALA* 4.0 0.9 - - - +
161A ALA 4.6 1.1 - - - +
162A TYR* 3.9 5.2 - - - -
184A VAL* 1.3 80.3 - - - +
186A ARG* 1.3 68.3 + - - +
187A LEU* 3.6 4.0 - - - -
188A CYS* 3.4 15.7 + - - -
189A TYR* 3.0 19.1 + - - +
1193A ZN 2.3 35.0 - - - -
18C ARG* 3.1 28.7 - - - +
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 3.8 5.5 - - - +
162A TYR* 3.2 19.6 + - + -
185A CYS* 1.3 75.2 - - - +
187A LEU* 1.3 74.5 + - + +
189A TYR* 3.3 16.1 + - - +
190A PHE* 3.4 17.6 - - + -
19C GLY* 3.9 18.5 + - - +
21C ILE* 3.5 16.4 - - - +
110C GLU* 3.2 23.2 + - - -
113C ALA* 3.6 22.4 - - - +
114C ASN* 3.1 31.9 + - - +
142C LEU 3.0 19.0 + - - -
144C GLU* 2.8 41.5 + - - +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A CYS* 3.4 8.5 - - - -
186A ARG* 1.3 87.5 - - + +
188A CYS* 1.3 65.7 + - - +
190A PHE* 3.3 6.6 + - + +
191A LYS* 3.3 28.5 + - + +
18C ARG* 3.3 52.2 - - - +
19C GLY 5.6 2.2 - - - +
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Residues in contact with CYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A CYS* 3.7 2.2 - - - -
155A GLU* 3.7 21.5 - - - +
156A CYS* 3.7 15.7 - - - -
164A LYS* 2.8 24.6 + - - -
184A VAL* 3.7 12.6 - - + -
185A CYS* 3.4 4.4 - - - +
186A ARG 3.4 0.4 - - - -
187A LEU* 1.3 79.1 - - - +
189A TYR* 1.3 63.3 + - - +
191A LYS* 3.3 28.8 + - + +
1193A ZN 2.4 35.2 - - - -
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Residues in contact with TYR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE 2.6 29.0 + - - -
129A GLN* 3.3 17.4 + - - +
130A ARG* 3.7 34.5 - - + -
162A TYR* 4.4 6.5 - - + -
163A THR 3.8 13.5 - - - -
164A LYS* 4.3 22.8 + - + +
184A VAL* 3.3 18.3 - - + +
185A CYS 3.0 20.4 + - - +
186A ARG* 3.4 9.0 - - - +
188A CYS* 1.3 77.9 - - - +
190A PHE* 1.3 84.5 + + + +
191A LYS 3.7 1.6 + - - +
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Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 3.4 30.1 - - - -
186A ARG* 3.4 26.0 + - + +
187A LEU* 3.3 7.8 + - + +
188A CYS 3.2 0.4 - - - -
189A TYR* 1.3 98.3 - + - +
191A LYS* 1.3 64.0 + - - +
110C GLU* 3.9 4.0 - - - -
114C ASN* 3.5 29.2 - - - -
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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