Contacts of the helix formed by residues 138 - 142 (chain T) in PDB entry 3L9J
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 ARG 138 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ARG* 4.1 1.8 - - - +
121C TYR* 2.7 30.2 + - - -
146C PRO* 3.4 20.5 - - - +
64T PHE* 3.5 15.7 - - + -
74T VAL* 3.9 10.5 - - - +
75T LEU 4.1 3.1 + - - +
76T LEU* 4.0 18.4 - - + -
136T ILE* 3.5 7.0 - - - +
137T ASN* 1.4 106.6 + - - +
139T PRO* 1.3 62.3 - - - +
140T ASP* 2.8 43.9 + - - +
141T TYR* 3.1 50.4 + - + -
142T LEU 3.5 1.7 + - - -
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Residues in contact with PRO 139 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ARG* 5.2 0.5 + - - -
24T GLY* 3.5 32.7 - - - +
25T GLN* 3.9 14.5 + - + -
26T LEU* 4.2 5.6 - - + +
136T ILE* 3.3 28.5 - - + +
137T ASN 3.5 8.7 - - - +
138T ARG* 1.3 89.6 - - - +
140T ASP* 1.3 58.8 + - + +
141T TYR 3.2 0.4 - - - -
142T LEU* 3.2 21.0 + - + +
144T PHE* 4.9 0.7 - - - -
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Residues in contact with ASP 140 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ARG* 2.9 29.1 + - - +
118C TRP* 3.9 2.9 - - - -
120C ARG* 2.8 42.0 + - - +
146C PRO* 3.5 13.2 - - - +
149C TRP* 3.9 16.4 - - + -
24T GLY* 4.3 1.9 + - - +
138T ARG* 2.8 50.6 + - - -
139T PRO* 1.3 82.6 - - + +
141T TYR* 1.3 59.9 + - - +
142T LEU 3.4 0.4 - - - -
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Residues in contact with TYR 141 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C TRP* 3.5 17.5 - + - -
119C SER 4.1 3.0 + - - -
120C ARG* 3.5 20.7 - - + +
121C TYR* 3.3 26.5 - - - -
64T PHE* 3.3 14.6 - - + -
65T LYS* 2.8 50.9 + - - +
66T GLY* 3.9 3.1 - - - -
68T GLY 5.6 0.7 - - - -
70T PRO* 4.6 4.7 - - - +
74T VAL* 3.8 19.1 - - + +
76T LEU* 3.8 17.7 - - + -
114T TRP* 3.7 22.2 + + - -
138T ARG* 3.1 48.8 + - + +
140T ASP* 1.3 78.3 + - - +
142T LEU* 1.3 63.4 + - - +
143T ASP 3.3 0.2 + - - -
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Residues in contact with LEU 142 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ARG* 4.3 4.0 + - - -
118C TRP* 3.5 14.6 - - - -
25T GLN 4.4 0.9 - - - +
26T LEU* 3.6 42.8 - - + +
62T VAL* 3.8 26.9 - - + -
63T LEU 3.6 15.5 - - - +
64T PHE* 4.5 4.3 - - + -
136T ILE* 3.8 19.3 - - + -
138T ARG 3.5 2.6 + - - -
139T PRO 3.2 16.2 + - - +
141T TYR* 1.3 76.1 - - - +
143T ASP* 1.3 58.9 + - - +
144T PHE* 3.6 37.4 + - + -
150T VAL* 3.8 16.6 - - + -
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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