Contacts of the helix formed by residues 137 - 142 (chain G) in PDB entry 3SHD
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 PRO 137 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PRO* 4.2 18.4 - - + -
139B GLU* 3.6 28.9 - - + +
136C TYR* 4.2 20.6 - - + +
64G HIS* 5.1 6.5 - - + -
65G PHE* 3.9 3.1 - - - +
136G TYR* 1.3 91.7 - - + +
138G LEU* 1.3 63.5 + - - +
139G GLU* 3.0 7.0 + - + +
140G MET* 3.3 25.7 - - + +
134L GLN* 4.7 14.6 - - - +
136L TYR* 5.8 2.5 - - - +
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Residues in contact with LEU 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLU* 3.3 12.8 + - - +
45G VAL* 4.3 20.0 - - + +
62G PRO* 3.3 25.1 - - + +
63G GLN* 3.5 16.1 + - - +
64G HIS* 3.5 30.0 - - - +
65G PHE* 3.9 3.1 - - - +
84G PHE* 3.7 24.0 - - + -
136G TYR 3.5 1.4 + - - -
137G PRO* 1.3 72.4 - - - +
139G GLU* 1.3 70.2 + - - +
140G MET 3.2 1.3 + - - -
141G ILE* 3.3 23.8 - - - +
142G GLY* 3.9 2.9 + - - -
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Residues in contact with GLU 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLN 5.9 2.2 - - - +
137B PRO* 4.7 10.1 - - + -
138B LEU* 5.2 7.4 - - + +
139B GLU* 2.6 40.2 - - - +
67C ARG* 3.0 31.0 + - - +
137G PRO* 3.0 4.1 - - + -
138G LEU* 1.3 82.2 - - - +
140G MET* 1.4 59.9 + - - +
141G ILE 3.0 5.6 - - - -
142G GLY* 2.9 25.8 + - - +
143G ASP* 5.0 6.8 + - - +
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Residues in contact with MET 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C PHE* 3.3 35.5 - - + -
66C ILE 3.7 8.5 - - - +
67C ARG* 3.7 8.5 - - - -
68C MET* 2.7 33.6 + - - +
136C TYR* 3.5 52.3 - - + -
140C MET* 3.5 12.8 - - + +
65G PHE* 4.2 13.0 - - + -
136G TYR* 4.0 15.0 - - + -
137G PRO* 3.3 23.0 + - + +
138G LEU 3.2 0.8 - - - -
139G GLU* 1.4 76.1 - - - +
141G ILE* 1.3 59.1 + - + +
142G GLY 3.5 0.2 - - - -
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Residues in contact with ILE 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C PHE* 5.5 0.9 - - + -
68C MET* 3.3 30.2 - - + +
70C GLN* 4.6 2.6 - - - +
140C MET* 5.4 0.9 - - + -
141C ILE* 5.4 3.4 - - + -
43G THR* 5.9 1.7 - - + +
44G LEU* 4.0 19.9 - - + +
45G VAL* 4.1 13.7 - - + -
65G PHE* 3.5 49.8 - - + -
82G PHE* 3.6 15.5 - - + -
84G PHE* 3.7 25.6 - - + -
138G LEU 3.3 16.4 - - - +
139G GLU 3.0 0.4 - - - -
140G MET* 1.3 85.2 - - + +
142G GLY* 1.3 60.7 + - - +
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Residues in contact with GLY 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ARG* 2.9 19.7 + - - +
69C HIS* 3.4 0.2 - - - -
70C GLN* 2.6 30.5 + - - -
43G THR* 6.2 1.1 - - - -
138G LEU 4.3 2.9 - - - -
139G GLU* 2.9 24.8 + - - -
141G ILE* 1.3 79.4 - - - +
143G ASP* 1.3 61.6 + - - -
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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