Contacts of the strand formed by residues 54 - 57 (chain L) in PDB entry 7JSL
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 GLU 54 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48L TRP* 3.2 19.4 - - - +
49L GLN* 3.1 28.7 + - - +
50L GLY* 4.0 4.0 + - - -
51L ASP* 3.2 38.9 + - + +
52L TYR 3.4 1.6 - - - -
53L GLY* 1.3 76.7 + - - +
55L PHE* 1.3 58.6 + - - +
97L THR* 3.7 23.1 - - + +
100L LYS* 3.9 20.5 + - - +
103L THR* 3.8 16.2 - - + +
104L TYR 3.5 5.2 - - - +
105L LYS* 3.4 22.8 + - + +
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Residues in contact with PHE 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L ILE* 4.2 18.8 - - + -
37L LEU* 3.8 20.4 - - + -
46L ILE* 3.8 28.5 - - + -
47L ALA 3.5 13.7 - - - +
48L TRP* 4.3 0.4 - - + -
49L GLN 4.2 3.8 - - - +
53L GLY 3.8 6.7 - - - -
54L GLU* 1.3 74.8 - - - +
56L VAL* 1.3 67.5 - - - +
57L ILE* 4.6 7.9 - - + -
85L LEU* 5.6 2.7 - - + -
94L LEU* 3.8 22.7 - - + -
102L PHE 3.6 0.3 - - - +
103L THR* 3.3 3.8 - - - +
104L TYR* 2.9 75.8 + + + -
106L PHE* 3.5 29.6 - + - -
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Residues in contact with VAL 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L ILE* 3.4 5.3 - - - +
47L ALA 3.0 30.3 + - - +
49L GLN* 3.5 44.2 - - + +
55L PHE* 1.3 76.6 - - - +
57L ILE* 1.3 76.0 + - - +
58L LYS* 3.6 9.6 + - + +
100L LYS* 6.0 1.1 - - + -
101L ARG 4.0 14.6 - - - +
102L PHE* 3.3 4.5 - - + -
103L THR* 3.4 25.4 - - + +
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Residues in contact with ILE 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L ILE* 6.5 1.3 - - + -
45L VAL 3.9 2.7 - - - +
46L ILE* 4.1 20.0 - - + -
55L PHE* 4.6 8.1 - - + -
56L VAL* 1.3 73.9 - - - +
58L LYS* 1.3 62.2 + - - +
59L ASP 3.7 1.1 - - - +
60L PRO* 3.4 34.7 - - + +
63L VAL* 3.6 27.8 - - + -
78L TYR* 3.9 24.9 - - + -
81L LEU* 5.2 5.2 - - + -
85L LEU* 4.9 7.4 - - + -
102L PHE* 3.1 36.4 + - + +
104L TYR* 4.2 20.2 - - + -
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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