Contacts of the strand formed by residues 148 - 152 (chain D) in PDB entry 3SPD
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 LEU 148 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D LEU* 3.4 4.6 - - - -
74D LEU* 2.8 56.2 + - + +
100D LEU* 4.2 28.3 - - + +
101D VAL* 6.1 0.4 - - + -
104D VAL* 4.6 5.6 - - + -
135D VAL* 3.5 24.2 - - + -
136D GLY* 3.5 33.4 - - - +
137D PHE* 3.7 31.5 - - + -
147D HIS* 1.3 71.3 - - - +
149D HIS* 1.3 63.6 + - - +
150D ILE* 3.6 2.1 + - + +
177D ILE* 3.9 12.3 - - + -
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Residues in contact with HIS 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ASP* 4.8 2.0 - - - -
71D HIS* 2.9 28.4 + + - +
72D LEU 3.5 4.7 - - - -
73D LEU* 3.5 6.5 - - + +
134D LYS 3.7 0.4 - - - +
135D VAL* 3.2 7.3 - - - +
136D GLY 2.8 42.1 + - - +
138D HIS* 3.7 34.2 + + - -
147D HIS* 3.8 33.7 + + - -
148D LEU* 1.3 72.2 - - - +
150D ILE* 1.3 61.2 + - - +
151D MET* 4.1 6.7 - - - -
169D PHE* 3.5 27.0 - + - -
174D PHE* 3.9 13.5 - + + -
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Residues in contact with ILE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU* 3.8 18.6 - - + -
70D MET* 4.0 7.9 - - + +
71D HIS* 3.7 0.5 - - - -
72D LEU* 2.8 44.5 + - + +
74D LEU* 3.7 29.8 - - + +
104D VAL* 3.8 20.6 - - + -
112D ILE* 4.2 34.1 - - + -
133D ILE* 4.3 11.9 - - + -
134D LYS 3.6 3.8 - - - -
135D VAL* 4.2 20.2 - - + -
148D LEU* 4.1 4.3 - - + +
149D HIS* 1.3 77.9 - - - +
151D MET* 1.3 61.2 + - - +
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Residues in contact with MET 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D LYS* 4.0 6.1 - - + -
68D SER* 4.0 6.7 - - - +
70D MET* 3.2 20.6 - - - +
71D HIS* 3.7 31.2 - - + +
133D ILE* 3.3 2.6 - - - -
134D LYS* 2.8 54.7 + - + +
149D HIS* 4.2 12.3 - - - -
150D ILE* 1.3 77.2 - - - +
152D THR* 1.3 68.9 + - - +
155D HIS* 3.8 18.4 - - + -
169D PHE* 3.3 38.8 - - + -
174D PHE* 4.3 3.6 - - - -
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Residues in contact with THR 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D SER* 2.7 24.1 + - - -
70D MET* 3.1 43.1 + - + -
116D ALA* 4.5 6.1 - - + -
120D LEU* 3.6 28.2 - - + +
129D LEU* 5.3 1.8 - - + -
132D TYR* 3.2 17.9 - - + +
133D ILE* 4.2 6.3 - - + -
134D LYS* 4.2 1.7 - - - -
151D MET* 1.3 82.7 - - - +
153D LEU* 1.3 58.7 + - - +
154D ASP* 2.6 24.5 + - - -
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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