Contacts of the helix formed by residues 137 - 142 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E HIS* 6.2 2.0 - - - +
64F HIS* 5.2 3.4 - - + -
65F PHE* 3.8 6.6 - - - +
135F ARG 4.8 0.4 - - - +
136F TYR* 1.4 94.5 - - + +
138F LEU* 1.3 65.9 + - - +
139F GLU* 3.9 27.4 - - + +
140F MET* 3.2 31.3 + - + +
136K TYR* 3.9 18.2 - - + +
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Residues in contact with LEU 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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45F VAL* 3.9 22.4 - - + -
62F PRO* 3.4 24.7 - - + +
63F GLN* 3.5 17.4 + - - +
64F HIS 3.8 17.0 - - - +
65F PHE* 4.0 2.5 - - - +
84F PHE* 3.6 35.4 - - + -
136F TYR 3.9 0.8 + - - -
137F PRO* 1.3 66.8 - - - +
139F GLU* 1.3 63.6 + - - +
140F MET 2.7 7.2 + - - -
141F ILE* 3.0 23.3 + - - +
142F GLY* 3.7 3.6 + - - -
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Residues in contact with GLU 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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137F PRO* 3.2 22.8 - - + +
138F LEU* 1.3 77.4 - - - +
140F MET* 1.3 62.9 + - + +
141F ILE 2.9 6.6 + - - -
142F GLY* 3.0 15.3 + - - +
67K ARG* 3.0 29.3 + - - +
134K GLN* 3.9 24.5 + - - +
136K TYR* 5.1 2.9 + - - +
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Residues in contact with MET 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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65F PHE* 4.0 9.2 - - + -
136F TYR* 3.7 17.3 - - + -
137F PRO* 3.2 17.8 + - + +
138F LEU 2.7 5.5 + - - -
139F GLU* 1.3 79.1 - - + +
141F ILE* 1.3 59.8 + - + +
65K PHE* 3.6 26.4 - - + -
66K ILE 5.4 0.2 - - - -
67K ARG* 3.4 11.6 - - - +
68K MET 2.9 23.2 + - - -
134K GLN* 6.0 0.9 - - - -
136K TYR* 3.4 54.3 - - + -
140K MET* 3.3 35.7 - - + -
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Residues in contact with ILE 141 (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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44F LEU* 4.1 22.0 + - + +
45F VAL* 4.9 6.7 - - + -
65F PHE* 4.3 36.1 - - + -
82F PHE* 4.1 13.7 - - + -
84F PHE* 4.2 24.5 - - + -
138F LEU* 3.0 17.2 + - - +
140F MET* 1.3 82.7 - - + +
142F GLY* 1.3 65.8 + - - +
143F ASP 3.9 0.5 + - - -
65K PHE* 4.7 6.7 - - + -
68K MET* 3.4 47.6 - - + +
70K GLN* 4.5 2.9 - - - +
82K PHE* 5.2 0.7 - - + -
141K ILE* 5.8 0.7 - - + -
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Residues in contact with GLY 142 (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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138F LEU 4.2 4.9 - - - -
139F GLU* 3.0 15.0 + - - -
141F ILE* 1.3 82.6 - - - +
143F ASP* 1.3 70.4 + - - -
144F PHE 3.7 0.2 + - - -
67K ARG* 3.0 20.1 + - - -
68K MET 3.6 2.7 + - - +
69K HIS* 3.8 0.5 - - - -
70K GLN 3.1 17.5 + - - -
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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