Contacts of the strand formed by residues 68 - 73 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLN* 4.0 8.7 - - - -
53B LEU* 3.6 19.7 - - + -
54B ILE* 4.5 9.4 - - + -
60B ARG* 3.5 21.6 + - - -
64B VAL* 3.8 29.6 - - + -
65B PRO* 3.5 21.5 + - + -
66B ASP 3.4 6.8 - - - +
67B ARG* 1.3 96.2 - - + +
69B SER* 1.3 63.7 + - - +
79B LEU* 4.9 4.3 - - + -
80B THR 3.4 4.9 - - - -
81B ILE* 3.5 29.8 - - + -
88B ASP* 3.2 31.9 - - - -
92B TYR* 3.6 20.2 - + - -
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 3.6 7.1 - - - +
58B SER 5.8 0.7 - - - -
60B ARG* 5.4 1.3 - - - +
66B ASP 5.2 1.6 + - - -
67B ARG 3.9 4.3 + - - -
68B PHE* 1.3 78.3 - - - +
70B GLY* 1.3 62.1 + - - +
71B SER* 5.1 1.1 + - - -
78B THR 3.6 1.2 - - - +
79B LEU* 3.6 2.2 - - - +
80B THR* 2.8 54.6 + - - +
82B SER* 5.4 1.7 + - - -
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Residues in contact with GLY 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TRP* 4.7 2.5 - - - -
54B ILE* 3.2 18.0 - - - +
57B ALA 3.1 20.0 - - - -
58B SER* 3.1 25.1 + - - +
69B SER* 1.3 75.5 - - - +
71B SER* 1.3 62.2 + - - -
78B THR 3.3 7.6 - - - -
79B LEU* 4.6 2.5 - - - -
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TRP* 5.4 0.5 + - - -
57B ALA* 4.3 5.5 - - - +
58B SER* 4.8 4.0 - - - -
69B SER* 6.3 0.7 - - - -
70B GLY* 1.3 75.2 - - - -
72B GLY* 1.3 68.0 + - - +
77B PHE* 3.6 11.6 - - - +
78B THR* 2.9 41.5 + - - +
80B THR* 4.6 4.5 + - - -
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 4.0 6.2 + - - -
57B ALA* 4.6 2.9 - - - +
58B SER* 6.1 0.5 - - - -
71B SER* 1.3 83.6 - - - +
73B SER* 1.3 64.9 + - - -
76B ASP 3.2 14.6 - - - -
77B PHE* 3.8 8.8 - - - -
78B THR* 4.8 1.1 - - - -
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 4.2 13.5 - - - +
37B ASN* 3.3 17.2 + - - -
72B GLY* 1.3 76.6 - - - -
74B GLY* 1.3 64.3 + - - +
75B THR 3.0 9.0 + - - -
76B ASP* 3.1 18.2 + - - +
77B PHE* 3.5 11.4 - - - -
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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