Contacts of the strand formed by residues 48 - 54 (chain N) in PDB entry 5HJD
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 48 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11N LEU* 5.5 0.7 - - + -
44N ILE* 3.1 27.0 + - + +
45N GLN* 3.4 14.6 - - - +
46N HIS 3.7 1.0 - - - -
47N PHE* 1.3 104.3 - - + +
49N GLU* 1.3 62.6 + - - +
50N LYS 3.5 23.8 - - - +
51N VAL* 3.9 7.4 - - + -
71N TYR* 3.8 26.1 + - + +
87N VAL* 3.8 16.2 - - + -
88N TYR 3.3 14.1 - - - +
89N PHE* 4.9 0.2 - - + -
90N LYS* 4.0 5.7 - - - -
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Residues in contact with GLU 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N VAL* 1.3 74.9 - - - +
50N LYS* 1.3 73.3 + - + +
67N LYS* 2.8 22.2 - - - +
68N ASP* 4.7 0.7 - - - +
71N TYR* 5.0 0.4 - - - -
88N TYR* 3.2 12.7 + - + +
89N PHE 3.9 14.6 - - - +
90N LYS* 3.6 30.9 - - + +
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Residues in contact with LYS 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N VAL* 3.5 8.3 - - - +
49N GLU* 1.3 87.7 + - + +
51N VAL* 1.3 64.2 + - - +
52N VAL* 4.1 7.4 - - + -
65N VAL* 3.9 21.8 - - + -
66N CYS 3.9 3.6 - - - +
67N LYS* 3.6 33.0 - - + +
71N TYR* 4.5 1.3 - - - -
88N TYR* 2.8 66.6 + - + +
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Residues in contact with VAL 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N VAL* 4.2 13.2 - - + -
44N ILE* 5.9 0.4 - - + -
48N VAL* 3.9 10.3 - - + -
50N LYS* 1.3 79.5 - - - +
52N VAL* 1.3 64.7 + - - +
53N PHE* 3.7 21.1 + - + -
65N VAL 4.0 0.2 - - - -
66N CYS* 2.9 34.5 + - - +
71N TYR* 3.6 29.6 - - + -
85N ILE* 3.7 26.7 - - + -
86N GLU 3.3 5.4 - - - +
87N VAL* 3.9 20.9 - - + -
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Residues in contact with VAL 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50N LYS* 4.1 8.1 - - + -
51N VAL* 1.3 78.4 - - - +
53N PHE* 1.3 62.7 + - - +
54N HIS* 3.3 32.8 + - + +
63N LYS* 4.0 10.8 - - + -
64N ARG 3.6 9.9 - - - +
65N VAL* 3.7 32.3 - - + -
84N PRO 3.7 1.6 - - - +
85N ILE* 3.4 4.3 - - - -
86N GLU* 2.7 43.1 + - + +
88N TYR* 3.7 25.6 - - + +
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Residues in contact with PHE 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N VAL* 3.6 26.2 - - + -
36N VAL* 4.2 10.8 - - + -
51N VAL* 3.7 27.6 - - + -
52N VAL* 1.3 72.5 - - - +
54N HIS* 1.3 60.6 + - - +
55N LEU* 3.6 7.6 + - + -
62N PRO 3.2 2.3 - - - +
63N LYS* 3.8 1.9 - - - -
64N ARG* 2.7 54.7 + - + +
66N CYS* 4.1 10.1 - - + -
71N TYR 3.4 24.9 - - - -
72N LYS* 3.8 22.7 - - - -
73N VAL* 4.8 8.5 - - + -
83N LEU* 4.0 10.8 - - + -
84N PRO 4.0 2.7 - - - -
85N ILE* 4.1 29.8 - - + -
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Residues in contact with HIS 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52N VAL* 3.3 27.7 - - + +
53N PHE* 1.3 72.2 - - - +
55N LEU* 1.3 66.6 + - - +
62N PRO 3.8 2.7 - - - -
63N LYS* 4.3 19.9 - - + +
82N ILE 4.5 0.9 - - - +
83N LEU* 3.4 9.8 - - - +
84N PRO* 2.9 61.0 + - + +
86N GLU* 3.5 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