Contacts of the helix formed by residues 137 - 142 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B GLN 5.7 0.2 - - - +
64B HIS* 5.0 6.5 - - + -
65B PHE* 4.1 2.3 - - - +
135B ARG 4.9 0.2 - - - +
136B TYR* 1.3 90.5 - - + +
138B LEU* 1.3 55.2 + - - +
139B GLU* 3.5 24.0 - - + +
140B MET* 2.7 50.2 + - + +
134C GLN* 6.4 1.6 - - + -
136C TYR* 5.4 4.7 - - - +
137G PRO* 4.2 23.3 - - + -
139G GLU* 4.7 8.3 - - + -
136L TYR* 4.7 9.4 - - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B VAL* 4.4 18.6 - - + +
61B GLN* 6.0 1.3 - - + -
62B PRO* 3.3 30.7 - - + +
63B GLN* 3.6 14.5 + - - +
64B HIS* 3.8 6.4 - - - +
65B PHE* 3.8 14.6 - - - +
84B PHE* 3.7 34.5 - - + -
136B TYR 3.4 3.2 + - - -
137B PRO* 1.3 64.2 - - - +
139B GLU* 1.3 65.2 + - - +
140B MET 2.6 17.6 + - - -
141B ILE* 3.1 24.1 + - - +
142B GLY* 3.7 2.3 + - - -
139G GLU* 5.2 6.2 - - + +
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PRO* 3.5 19.4 - - + +
138B LEU* 1.3 87.2 + - - +
140B MET* 1.3 58.6 + - + -
141B ILE 3.3 0.4 - - - -
142B GLY* 3.3 10.0 + - - +
137G PRO* 3.6 15.5 - - + -
138G LEU* 3.3 12.9 + - + +
139G GLU* 2.6 57.4 + - - +
67L ARG* 2.9 33.5 + - - +
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PHE* 4.1 17.7 - - + -
136B TYR* 4.3 6.7 - - + -
137B PRO* 2.7 35.9 + - + +
138B LEU 2.6 7.3 + - - -
139B GLU* 1.3 74.5 - - - +
141B ILE* 1.3 59.3 + - - +
142B GLY 3.6 0.4 - - - -
65L PHE* 3.9 12.0 - - + -
66L ILE 4.1 10.8 - - - +
67L ARG* 3.7 10.9 - - + +
68L MET 3.3 21.7 + - - -
134L GLN* 5.4 4.5 - - - +
136L TYR* 3.6 37.9 - - + +
140L MET* 3.3 32.1 - - - -
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.6 23.1 - - + +
45B VAL* 4.1 13.2 - - + -
65B PHE* 3.7 42.2 - - + -
82B PHE* 3.7 21.5 - - + -
84B PHE* 3.9 21.3 - - + -
138B LEU 3.4 13.9 - - - +
140B MET* 1.3 83.1 - - + +
142B GLY* 1.3 62.2 + - - +
65L PHE* 5.4 3.8 - - + -
68L MET* 2.9 43.0 - - + +
70L GLN* 4.6 2.1 - - - +
82L PHE* 5.5 0.9 - - + -
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B THR* 6.3 1.1 - - - -
45B VAL* 6.0 2.9 - - - -
138B LEU 3.7 3.3 + - - -
139B GLU* 3.3 17.2 + - - -
141B ILE* 1.3 81.7 - - - +
143B ASP* 1.3 64.6 + - - -
67L ARG* 2.9 24.8 + - - +
69L HIS* 3.5 0.3 - - - -
70L GLN* 3.0 22.1 + - - -
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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