Contacts of the strand formed by residues 46 - 52 (chain H) in PDB entry 6PB4
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 SER 46 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45H GLY* 1.3 73.7 - - - -
47H VAL* 1.3 62.6 + - - +
63H TYR* 5.5 2.9 - - - -
64H LEU 3.5 5.8 - - - -
65H ASN* 2.8 21.0 + - - -
89H LYS* 3.2 33.1 + - - -
90H THR* 2.8 31.5 + - - +
92H CYS* 3.1 11.2 - - - -
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Residues in contact with VAL 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H LEU* 5.3 6.5 - - + -
42H ILE* 4.2 22.2 - - + -
46H SER* 1.3 81.3 - - - +
48H ALA* 1.3 64.3 + - - +
49H VAL* 4.8 2.2 - - + -
63H TYR* 3.0 8.9 - - - +
64H LEU* 2.8 35.7 + - + +
86H VAL* 3.3 34.1 - - + +
87H ARG 3.4 19.5 - - - +
88H ALA* 3.9 11.9 - - + +
89H LYS* 4.0 4.7 - - - +
92H CYS* 3.9 13.0 - - + -
94H VAL* 5.8 3.4 - - + -
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Residues in contact with ALA 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H VAL* 1.3 72.6 - - - +
49H VAL* 1.3 62.5 + - - +
50H LEU* 3.2 11.3 - - + +
60H ILE* 4.5 13.0 - - + -
62H SER 3.7 7.9 - - - +
63H TYR* 4.2 4.5 - - + +
86H VAL* 3.4 1.0 - - - -
87H ARG* 2.9 69.1 + - - +
89H LYS* 4.9 4.3 - - + -
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Residues in contact with VAL 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H VAL* 4.8 2.7 - - + -
48H ALA* 1.3 74.8 - - - +
50H LEU* 1.3 62.8 + - - +
60H ILE* 3.8 0.2 - - - +
61H LEU* 3.0 9.0 + - + +
62H SER* 2.9 42.9 + - - +
64H LEU* 3.6 28.5 - - + -
70H ILE* 4.6 7.6 - - + -
84H ALA* 4.1 11.0 - - + -
85H TRP 3.3 9.6 - - - +
86H VAL* 3.9 25.4 - - + -
301H CMP 3.2 32.8 - - + +
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Residues in contact with LEU 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H ALA* 3.2 26.0 - - + +
49H VAL* 1.3 76.1 - - - +
51H ILE* 1.3 69.2 + - - +
58H GLU* 3.1 25.8 - - + +
59H MET 3.2 13.7 - - - +
60H ILE* 3.6 21.5 - - + -
61H LEU* 4.1 2.5 - - - +
84H ALA* 3.4 0.3 - - - +
85H TRP* 3.0 55.6 + - + +
87H ARG* 4.0 26.7 - - + +
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Residues in contact with ILE 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G SER* 5.6 7.9 - - - +
32H GLN* 4.4 6.1 - - - +
50H LEU* 1.3 81.2 - - - +
52H LYS* 1.3 64.9 + - - +
58H GLU* 3.0 8.8 - - - +
59H MET* 2.7 47.0 + - + +
61H LEU* 3.6 37.5 - - + -
83H SER 4.3 7.0 - - - +
84H ALA* 3.6 20.0 - - + -
85H TRP* 4.1 8.1 - - - -
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Residues in contact with LYS 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H GLN* 4.5 10.4 + - - +
51H ILE* 1.3 81.5 - - - +
53H ASP* 1.3 78.4 + - - +
54H GLU* 3.5 35.5 + - - +
56H GLY* 3.8 15.0 - - - +
57H LYS 3.4 10.1 - - - +
58H GLU* 3.8 5.6 - - + +
85H TRP* 3.4 36.8 - - + -
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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