Contacts of the strand formed by residues 45 - 52 (chain B) in PDB entry 6S6A
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 VAL 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE 3.5 3.8 + - - +
44B ASP* 1.3 92.4 + - - +
46B GLU* 1.3 57.7 + - - +
47B HIS* 3.6 27.9 + - + +
61B TRP* 3.5 51.8 - - + -
62B ASP 3.8 4.0 - - - -
63B CYS* 4.2 8.1 - - - -
73B TYR* 4.1 9.2 - - + -
77B GLN* 4.8 1.8 - - - +
80B ASN* 6.2 0.2 - - - +
81B ILE* 3.7 27.6 - - + -
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Residues in contact with GLU 46 (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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21B THR* 4.4 4.0 - - - +
24B ARG* 3.2 29.9 + - - +
42B THR* 3.8 28.5 + - + +
43B ILE 4.8 0.4 + - - +
44B ASP 3.8 1.8 + - - -
45B VAL* 1.3 68.9 - - - +
47B HIS* 1.3 72.2 + - - +
48B SER* 3.9 3.8 + - - -
60B LEU 4.1 0.5 - - - +
62B ASP* 3.2 31.4 + - + +
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Residues in contact with HIS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.6 28.3 + - + -
46B GLU* 1.3 78.6 - - - +
48B SER* 1.3 61.2 + - - +
49B HIS* 4.3 16.8 - - + +
60B LEU 3.4 6.7 - - - +
61B TRP* 3.4 58.7 - + - +
80B ASN* 6.2 1.1 - - - -
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 3.6 42.9 + - - +
28B PHE* 5.5 2.4 - - - +
46B GLU 4.3 1.3 - - - -
47B HIS* 1.3 77.2 - - - +
49B HIS* 1.3 67.2 + - - +
50B VAL* 3.4 14.6 + - - +
58B LEU 3.7 2.6 - - - +
60B LEU* 3.1 30.5 + - - +
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Residues in contact with HIS 49 (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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47B HIS* 4.3 18.0 - - + +
48B SER* 1.3 78.2 - - - +
50B VAL* 1.3 60.0 + - - +
51B ARG 4.3 0.7 + - - -
57B VAL* 4.6 8.6 - - + +
58B LEU 3.3 5.4 - - - +
59B ASN* 2.6 39.3 + - + +
60B LEU 5.0 0.4 - - - -
61B TRP* 5.4 0.2 + - - -
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Residues in contact with VAL 50 (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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28B PHE* 3.8 44.9 - - + +
48B SER* 3.8 14.4 - - - +
49B HIS* 1.3 71.8 - - - +
51B ARG* 1.3 74.6 + - - +
52B PHE* 3.8 14.7 + - + +
57B VAL* 3.1 8.2 - - - +
58B LEU* 2.7 48.8 + - + +
60B LEU* 4.4 7.2 - - + -
207B GLU* 5.9 0.7 - - - +
210B THR* 5.4 2.9 - - + -
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Residues in contact with ARG 51 (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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49B HIS 4.3 1.4 + - - -
50B VAL* 1.3 80.6 - - - +
52B PHE* 1.3 60.6 + - - +
53B LEU 4.0 1.2 + - - -
54B GLY* 4.2 23.1 - - - +
56B LEU 4.0 2.0 - - - +
57B VAL* 4.5 18.4 - - + +
207B GLU* 4.4 8.0 - - - +
269B ASN* 5.4 5.3 - - - +
302B ARG* 5.9 3.4 - - - +
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Residues in contact with PHE 52 (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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28B PHE* 4.7 2.7 - + - -
50B VAL* 4.5 9.4 - - + -
51B ARG* 1.3 72.9 - - - +
53B LEU* 1.3 81.9 + - + +
54B GLY 2.9 7.1 + - - -
56B LEU* 2.7 52.4 + - + +
58B LEU* 4.4 17.5 - - + -
177B VAL* 3.4 32.8 - - + -
181B ILE* 4.5 1.8 - - + -
207B GLU* 3.2 42.8 - - + -
210B THR* 3.5 19.7 - - + -
212B LEU* 4.0 11.0 - - + -
214B ILE* 3.7 23.6 - - + -
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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