Contacts of the strand formed by residues 54 - 57 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H TRP* 3.1 18.0 - - - +
49H GLN* 3.2 29.6 + - - +
50H GLY* 3.7 14.8 + - - -
51H ASP* 3.7 26.3 + - + +
52H TYR 3.6 1.8 - - - -
53H GLY* 1.3 77.9 - - - +
55H PHE* 1.3 58.5 + - - +
97H THR* 3.6 28.1 - - + +
100H LYS* 4.1 14.9 + - - +
103H THR* 3.9 14.0 - - + +
104H TYR 3.5 5.6 - - - +
105H LYS* 3.4 23.9 + - + +
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Residues in contact with PHE 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ILE* 4.4 15.3 - - + -
37H LEU* 3.7 19.7 - - + -
46H ILE* 3.7 29.2 - - + -
47H ALA 3.4 15.9 - - - +
48H TRP* 4.1 1.8 - + + +
49H GLN 4.1 2.5 - - - +
53H GLY 3.9 6.5 - - - -
54H GLU* 1.3 73.6 - - - +
56H VAL* 1.3 68.2 + - - +
57H ILE* 4.6 8.7 - - + -
85H LEU* 5.8 2.7 - - + -
94H LEU* 3.9 13.2 - - + -
102H PHE 3.8 0.2 - - - +
103H THR* 3.4 4.9 - - - +
104H TYR* 3.0 73.6 + + + +
106H PHE* 3.4 35.4 - + - -
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Residues in contact with VAL 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ILE* 3.2 19.9 - - - +
47H ALA 3.0 19.2 + - - +
49H GLN* 4.1 34.1 - - + +
55H PHE* 1.3 78.0 - - - +
57H ILE* 1.3 76.8 + - - +
58H LYS* 3.7 12.5 + - + +
100H LYS* 6.1 0.9 - - + -
101H ARG 4.0 15.0 - - - +
102H PHE* 3.4 5.2 - - + -
103H THR* 3.4 25.4 - - + +
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Residues in contact with ILE 57 (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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33H ILE* 6.4 1.3 - - + -
45H VAL 3.8 2.5 - - - -
46H ILE* 4.1 19.3 - - + -
55H PHE* 4.6 6.3 - - + -
56H VAL* 1.3 76.1 - - - +
58H LYS* 1.3 63.4 + - - +
59H ASP 3.8 0.4 - - - -
60H PRO* 3.4 36.4 - - + +
63H VAL* 3.5 29.2 - - + -
78H TYR* 4.0 25.1 - - + -
81H LEU* 5.2 2.7 - - + -
85H LEU* 4.8 8.3 - - + -
102H PHE* 3.2 31.8 + - + +
104H TYR* 4.3 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