Contacts of the strand formed by residues 68 - 73 (chain L) in PDB entry 4JZJ
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 PHE 68 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L GLN* 4.1 10.5 - - - -
53L LEU* 3.6 26.0 - - + -
54L ILE* 5.0 4.0 - - + -
60L ARG* 3.2 24.2 + - - -
64L VAL* 3.7 20.0 - - + -
65L PRO* 3.1 38.4 + - + +
66L ASP 3.8 3.5 - - - +
67L ARG* 1.3 88.5 - - + +
69L SER* 1.3 64.1 + - - +
79L LEU* 4.7 9.9 - - + -
80L THR 3.6 2.0 - - - -
81L ILE* 3.5 29.4 - - + -
88L ASP* 3.7 29.4 - - - -
92L TYR* 3.7 14.8 - + - -
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Residues in contact with SER 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L ILE* 4.6 5.4 - - - -
58L SER 5.6 0.9 - - - -
60L ARG* 5.3 2.0 - - - +
66L ASP 5.1 4.0 - - - -
67L ARG 3.9 1.5 + - - -
68L PHE* 1.3 76.4 - - - +
70L GLY* 1.3 64.5 + - - +
71L SER* 5.7 1.0 - - - -
78L THR* 3.9 0.5 - - - +
79L LEU* 3.7 8.8 - - - +
80L THR* 2.9 49.1 + - - +
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Residues in contact with GLY 70 (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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41L TRP* 4.8 2.9 - - - -
54L ILE* 4.2 13.8 - - - +
57L ALA 3.3 21.1 - - - -
58L SER* 3.5 18.6 + - - +
69L SER* 1.3 80.4 + - - +
71L SER* 1.3 63.0 + - - -
78L THR* 3.2 9.4 - - - -
79L LEU* 4.6 1.8 - - - -
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Residues in contact with SER 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L TRP* 5.6 0.2 + - - -
57L ALA* 3.5 7.4 + - - +
58L SER* 4.8 5.4 - - - -
69L SER* 5.7 1.1 - - - -
70L GLY* 1.3 76.8 - - - -
72L GLY* 1.3 65.9 + - - +
77L PHE* 3.5 10.7 - - - +
78L THR* 3.0 47.6 + - - +
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Residues in contact with GLY 72 (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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37L ASN* 3.6 10.6 + - - -
57L ALA* 4.7 2.8 - - - +
58L SER* 6.1 0.3 - - - -
71L SER* 1.3 82.4 + - - +
73L SER* 1.3 66.0 + - - -
76L ASP 3.3 12.6 - - - -
77L PHE* 3.9 6.9 - - - -
78L THR* 5.0 0.4 - - - -
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Residues in contact with SER 73 (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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30L LEU* 4.3 9.9 - - - +
37L ASN* 3.3 23.3 + - - -
72L GLY* 1.3 76.1 - - - -
74L GLY* 1.3 60.2 + - - +
75L THR 2.9 9.9 + - - -
76L ASP* 3.2 13.7 + - - +
77L PHE* 3.7 6.0 - - - -
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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