Contacts of the strand formed by residues 43 - 47 (chain D) in PDB entry 1SQV
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 MET 43 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D TYR* 3.3 36.1 + - + +
42D SER* 1.3 71.8 - - - +
44D ASP* 1.3 59.4 + - - +
45D TYR 3.1 9.4 + - - -
46D VAL* 3.7 34.3 + - + +
91D PHE* 3.0 56.5 + - + +
93D LYS 5.3 1.2 - - - +
113D LEU* 4.1 9.0 - - - +
114D SER* 3.5 25.1 - - - +
189D PHE* 3.6 34.1 - - + -
190D LEU* 4.4 6.1 - - - -
193D ALA* 4.5 2.7 - - + -
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Residues in contact with ASP 44 (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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42D SER* 3.4 25.1 - - - -
43D MET* 1.3 71.7 + - - +
45D TYR* 1.3 82.0 + - + +
90D TYR* 3.2 33.3 - - - +
91D PHE 4.2 7.2 - - - +
92D PRO* 5.1 9.4 - - - +
93D LYS 5.3 0.9 + - - -
112D ASP* 4.5 10.4 - - - +
114D SER* 3.5 7.3 + - - +
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Residues in contact with TYR 45 (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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63C PHE* 3.6 37.6 - + - +
64C SER* 3.3 32.9 + - - -
67C THR* 3.8 23.6 - - + -
71C ARG* 3.8 29.4 + - - +
72C ASP* 5.6 0.3 - - - +
258C PRO* 5.0 4.0 - - + +
43D MET 3.1 1.0 + - - -
44D ASP* 1.3 95.9 - - + +
46D VAL* 1.3 64.2 + - - +
50D HIS* 3.6 15.1 + - - -
90D TYR* 3.7 20.3 - + - -
112D ASP* 4.8 6.1 + - - -
114D SER* 3.7 26.8 + - - -
115D TYR* 4.6 11.0 - + + -
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Residues in contact with VAL 46 (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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71C ARG* 3.8 19.3 - - - +
43D MET* 3.7 33.1 + - + +
45D TYR* 1.3 79.7 - - - +
47D ALA* 1.3 68.3 + - - +
50D HIS* 3.5 11.9 - - + -
90D TYR* 3.3 10.0 - - - +
91D PHE* 3.1 41.2 + - + -
114D SER* 4.7 2.2 - - - -
189D PHE* 5.9 0.2 - - + -
192D TRP* 3.7 35.7 - - + -
193D ALA* 4.5 13.2 - - + +
196D PRO* 6.3 0.2 - - + -
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Residues in contact with ALA 47 (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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46D VAL* 1.3 76.0 - - - +
48D TYR* 1.3 61.0 + - - +
49D ARG* 3.3 15.9 - - + +
50D HIS* 3.0 40.3 + - + +
51D LEU* 3.6 11.8 + - - +
87D LEU 4.1 6.1 - - - +
89D ASP 3.4 18.4 - - - +
90D TYR* 3.9 12.8 - - + +
91D PHE* 3.6 8.8 - - - -
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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