Contacts of the helix formed by residues 137 - 142 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A HIS* 4.8 0.7 - - + -
65A PHE* 4.0 2.2 - - - +
136A TYR* 1.3 93.8 - - + +
138A LEU* 1.3 65.6 + - - +
139A GLU* 4.0 9.4 - - + +
140A MET* 2.9 33.2 + - + +
137D PRO* 3.9 29.6 - - + -
139D GLU* 3.3 38.1 - - + +
134E GLN* 6.2 3.4 - - + -
136E TYR* 5.2 5.2 - - - +
136I TYR* 4.6 11.0 - - - +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 4.7 25.1 - - + -
61A GLN* 6.1 1.6 - - + -
62A PRO* 3.3 29.6 - - + +
63A GLN* 4.1 11.0 + - - +
64A HIS* 4.0 11.6 - - - +
65A PHE* 4.1 4.9 - - - +
84A PHE* 3.9 31.4 - - + -
136A TYR 3.5 4.2 + - - -
137A PRO* 1.3 63.3 - - - +
139A GLU* 1.3 54.3 + - + +
140A MET 2.5 18.5 + - - -
141A ILE* 3.0 20.6 + - - +
142A GLY* 3.4 7.1 + - - -
139D GLU* 6.0 0.2 - - - +
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PRO* 3.1 10.5 - - + +
138A LEU* 1.3 76.7 - - + +
140A MET* 1.3 58.3 + - - +
141A ILE 3.3 1.4 + - - -
142A GLY* 3.3 7.7 + - - +
63D GLN 3.7 14.4 - - - +
64D HIS* 4.4 8.7 + - - -
137D PRO* 3.3 22.3 - - + +
138D LEU* 2.7 46.9 + - + +
139D GLU* 3.5 6.6 + - + +
67I ARG* 3.0 37.8 + - - +
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Residues in contact with MET 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PHE* 3.9 17.5 - - + -
136A TYR* 3.7 20.6 - - + -
137A PRO* 2.9 27.8 + - + +
138A LEU 2.5 9.2 + - - +
139A GLU* 1.3 73.8 - - - +
141A ILE* 1.3 59.7 - - + +
142A GLY 3.6 0.2 - - - -
65I PHE* 3.3 35.2 - - + -
66I ILE 3.9 8.7 - - - +
67I ARG* 3.7 11.3 - - - +
68I MET 3.0 25.9 + - - +
134I GLN* 5.1 4.0 - - - +
136I TYR* 3.3 46.7 - - + -
140I MET* 3.7 9.2 - - - -
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A THR* 5.6 0.5 - - - +
44A LEU* 3.7 31.6 - - + +
45A VAL* 4.5 10.5 - - + -
65A PHE* 3.9 39.0 - - + -
82A PHE* 3.5 23.6 - - + -
84A PHE* 4.1 19.5 - - + -
138A LEU* 3.0 11.2 + - - +
140A MET* 1.3 81.2 - - + +
142A GLY* 1.3 68.8 + - - +
65I PHE* 5.3 4.3 - - + -
68I MET* 3.1 36.2 - - + +
70I GLN* 4.3 2.9 - - - +
82I PHE* 5.5 0.7 - - + -
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A THR* 5.4 2.7 - - - -
45A VAL* 5.5 3.1 - - - -
138A LEU 3.4 7.9 + - - -
139A GLU* 3.3 15.0 + - - -
141A ILE* 1.3 85.3 - - - +
143A ASP* 1.3 65.3 + - - -
67I ARG* 2.9 25.0 + - - +
69I HIS* 3.9 0.2 - - - -
70I GLN* 3.3 14.9 + - - -
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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