Contacts of the helix formed by residues 139 - 145 (chain P) in PDB entry 3J0S
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 139 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328E LYS* 5.7 5.4 - - - -
77P ASP* 5.1 5.8 - - - -
104P TRP* 3.4 19.5 - - - -
137P ALA* 3.4 3.2 - - - +
138P ASN* 1.3 88.8 - - - +
140P TYR* 1.3 78.7 + - - +
141P GLU* 3.3 20.1 + - + +
142P GLU* 3.5 10.4 + - + +
143P VAL* 3.4 13.5 + - - +
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Residues in contact with TYR 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72P VAL* 3.2 41.0 - - + +
73P LYS* 4.6 7.3 + - + -
75P LEU 4.1 3.6 - - - -
76P PRO* 2.9 31.1 - - + +
77P ASP* 3.6 36.1 - - + -
78P LYS* 5.3 3.8 - - + +
104P TRP* 3.9 4.9 - + - -
139P CYS* 1.3 80.2 - - - +
141P GLU* 1.3 54.9 + - + +
143P VAL* 3.3 4.4 + - + +
144P LYS* 2.7 44.9 + - + +
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Residues in contact with GLU 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139P CYS* 3.3 14.5 - - + -
140P TYR* 1.3 79.0 - - + +
142P GLU* 1.3 63.4 + - + +
144P LYS* 3.7 12.3 - - + +
145P ASP* 3.0 39.9 + - - +
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Residues in contact with GLU 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E ARG* 5.0 2.4 + - - -
295E ALA* 4.8 6.2 - - - +
326E LYS* 4.7 15.6 - - - +
328E LYS* 3.2 36.4 + - - +
68P TYR* 4.4 0.7 + - - -
136P GLN 4.1 4.7 - - - +
137P ALA* 3.4 32.8 - - + +
138P ASN* 4.1 8.2 + - - +
139P CYS* 3.5 9.3 + - + +
140P TYR 3.3 0.6 - - - -
141P GLU* 1.3 80.1 - - + +
143P VAL* 1.3 62.2 + - - +
145P ASP* 3.7 7.0 + - - +
148P THR* 3.2 37.3 + - + +
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Residues in contact with VAL 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P TYR* 2.8 32.0 + - - +
71P PHE* 4.0 27.4 - - + -
72P VAL* 3.6 25.3 - - + +
75P LEU* 5.0 5.6 - - + -
102P ILE* 5.7 5.2 - - + -
103P PHE 5.9 0.2 - - - +
104P TRP* 3.3 39.9 - - + -
137P ALA* 3.5 14.1 - - + +
139P CYS 3.4 1.5 + - - +
140P TYR* 3.3 8.4 + - - +
142P GLU* 1.3 77.3 - - - +
144P LYS* 1.3 60.7 + - - +
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Residues in contact with LYS 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P TYR* 4.0 9.7 - - - +
72P VAL* 3.7 28.4 - - + +
73P LYS* 4.7 14.8 - - - +
140P TYR* 2.7 30.6 + - - +
141P GLU* 3.7 10.8 - - + +
143P VAL* 1.3 75.1 - - - +
145P ASP* 1.3 67.8 + - - +
146P ARG* 3.5 11.4 + - - -
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Residues in contact with ASP 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P TYR* 3.6 18.0 + - - -
141P GLU* 3.0 27.3 + - - +
142P GLU* 3.7 11.2 + - - +
143P VAL 3.4 0.8 - - - -
144P LYS* 1.3 86.9 - - - +
146P ARG* 1.3 63.7 + - - +
147P CYS* 3.4 10.6 + - + +
148P THR* 3.5 15.2 + - - +
149P LEU 4.1 0.2 + - - -
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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