Contacts of the helix formed by residues 134 - 140 (chain f) in PDB entry 5T0J
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 GLN 134 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89f LEU* 4.7 10.7 - - - +
90f LEU* 5.3 5.3 - - - +
93f ALA* 5.3 7.5 - - - +
123f PHE* 3.6 41.2 - - + -
126f CYS* 3.4 31.2 + - + +
131f VAL* 3.3 31.5 - - - +
132f GLN* 3.9 11.1 + - - +
133f LYS* 1.3 81.0 - - - +
135f MET* 1.3 63.8 + - + +
136f ALA* 3.0 12.7 + - - +
137f PHE* 3.4 15.3 + - - +
138f MET* 3.9 9.9 + - - +
148f LEU* 5.2 2.9 - - + +
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Residues in contact with MET 135 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89f LEU* 6.4 1.6 - - - -
92f CYS* 4.4 4.9 - - - +
93f ALA* 3.7 44.6 - - + +
96f VAL* 3.7 33.9 - - + -
97f PHE* 4.2 6.7 - - + +
100f PHE* 5.9 0.2 - - + -
119f VAL* 4.4 26.0 - - + -
134f GLN* 1.3 76.1 - - - +
136f ALA* 1.3 58.1 + - - +
137f PHE 3.2 0.7 - - - -
138f MET* 3.6 10.5 - - - -
139f LEU* 2.6 56.5 + - + +
144f VAL* 5.4 0.9 - - - -
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Residues in contact with ALA 136 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123f PHE* 5.7 1.1 - - + -
134f GLN* 3.0 3.9 + - + +
135f MET* 1.3 77.6 - - - +
137f PHE* 1.3 58.5 + - - +
140f GLY* 3.3 23.6 + - - -
141f ARG 4.0 5.5 + - - +
144f VAL* 3.9 28.4 - - + +
145f PHE* 5.1 4.1 - - + +
148f LEU* 3.6 47.3 - - + -
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Residues in contact with PHE 137 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132f GLN* 6.3 1.1 - - - -
133f LYS* 4.2 32.3 - - + -
134f GLN 3.4 11.4 + - - +
135f MET 3.2 0.2 - - - -
136f ALA* 1.3 76.2 - - - +
138f MET* 1.3 67.7 + - + +
140f GLY* 3.8 7.2 + - - -
145f PHE* 5.3 8.1 - + - -
148f LEU* 3.7 37.7 - - + -
160f GLU* 6.6 0.2 - - - -
161f ILE* 4.4 36.7 - - + +
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Residues in contact with MET 138 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90f LEU* 5.8 4.5 - - + +
93f ALA* 3.9 29.8 - - + +
94f LEU* 3.7 31.4 - - + -
97f PHE* 3.3 34.1 - - + -
133f LYS* 3.4 44.6 - - + +
134f GLN 4.0 5.4 - - - +
135f MET* 3.2 12.6 + - + +
137f PHE* 1.3 82.5 - - + +
139f LEU* 1.3 62.9 + - - +
140f GLY* 4.5 0.2 - - - -
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Residues in contact with LEU 139 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97f PHE* 3.5 30.7 - - + -
100f PHE* 4.3 27.4 - - + -
101f SER* 5.3 4.9 - - - +
109f LEU* 4.6 17.0 - - + -
116f MET* 4.6 10.1 - - + -
119f VAL* 6.1 3.6 - - + -
135f MET* 2.6 40.6 + - + +
138f MET* 1.3 75.0 - - - +
140f GLY* 1.3 58.3 + - - +
141f ARG* 3.4 31.8 + - + +
144f VAL* 5.7 2.0 - - + -
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Residues in contact with GLY 140 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136f ALA 3.3 15.4 + - - -
137f PHE 4.3 5.4 - - - -
138f MET 3.3 3.4 - - - -
139f LEU* 1.3 77.7 - - - +
141f ARG* 1.3 64.4 + - - +
142f HIS* 3.3 23.9 + - - -
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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