Contacts of the strand formed by residues 88 - 94 (chain J) in PDB entry 4R2G
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 ALA 88 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38J ARG* 4.2 8.5 - - + -
39J GLN 3.1 25.4 - - - +
40J SER* 3.3 13.5 - - - +
41J PRO* 4.7 1.8 - - - -
86J ASP 2.9 11.2 + - - +
87J THR* 1.3 77.5 - - - +
89J ILE* 1.3 66.0 + - - +
90J TYR* 3.9 12.7 - - + -
108J ALA* 3.6 2.1 - - - +
109J VAL* 2.9 31.5 + - - +
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Residues in contact with ILE 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I GLY* 4.7 21.8 - - - +
38J ARG* 3.2 3.5 - - - -
39J GLN* 2.9 48.5 + - + +
88J ALA* 1.3 80.0 - - - +
90J TYR* 1.3 61.7 + - - +
91J PHE* 3.4 34.1 - - + -
106J GLY* 4.3 2.2 - - - -
107J THR 3.5 19.7 - - - +
108J ALA* 4.3 15.7 - - + +
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Residues in contact with TYR 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J GLU* 3.9 1.7 - - - +
18J LEU* 3.4 25.1 - - + +
20J VAL* 4.3 14.4 - - + -
36J TRP* 4.5 3.8 - + + -
37J ILE 3.8 2.0 - - - -
38J ARG* 3.0 39.6 + - + -
48J ILE* 4.5 3.6 - - + -
80J LEU* 3.7 25.1 - - + -
82J LEU* 3.2 20.1 - - + +
86J ASP 2.7 29.9 + - - -
88J ALA* 3.9 17.7 - - + -
89J ILE* 1.3 75.9 - - - +
91J PHE* 1.3 60.4 + - - +
106J GLY 3.5 1.4 - - - -
107J THR* 2.8 49.7 + - + +
109J VAL* 4.0 16.2 - - + -
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Residues in contact with PHE 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I HIS* 4.7 0.7 - + - -
41I GLY 5.6 0.4 - - - -
42I GLN 3.7 15.3 - - - -
43I ALA* 3.5 33.0 - - + -
44I PRO* 4.0 9.2 - - + -
6J GLU* 3.6 4.7 - - - +
36J TRP* 3.1 11.5 - - - -
37J ILE* 2.9 43.6 + - + +
38J ARG* 4.5 0.4 - - - -
39J GLN* 4.3 19.1 - - + -
45J LEU* 4.8 2.9 - - + -
89J ILE* 3.4 37.2 - - + -
90J TYR* 1.3 72.6 - - - +
92J CYS* 1.3 60.7 + - - +
103J TRP* 3.9 29.2 - + + -
104J GLY 4.4 2.2 - - - +
105J LYS 3.7 10.5 - - - -
106J GLY* 3.6 16.8 - - - -
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Residues in contact with CYS 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 3.8 6.8 - - - +
6J GLU* 2.7 19.2 + - - +
22J CYS* 2.0 57.0 - - + -
35J THR 3.2 10.8 - - - +
36J TRP* 3.6 23.1 - - + -
78J LEU* 4.2 8.7 - - + -
91J PHE* 1.3 74.4 - - - +
93J ALA* 1.3 61.8 + - - +
104J GLY 2.9 24.1 + - - -
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Residues in contact with ALA 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 3.7 4.9 - - - -
34J TRP* 3.7 7.4 - - - -
35J THR* 2.9 36.5 + - + +
37J ILE* 5.5 0.9 - - + -
91J PHE 4.4 0.2 + - - -
92J CYS* 1.3 76.2 - - - +
94J THR* 1.3 68.2 + - - +
100J MET* 4.3 11.2 - - - +
102J VAL 3.1 16.6 - - - +
103J TRP* 3.7 29.6 - - + -
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Residues in contact with THR 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J VAL* 4.7 5.8 - - + -
4J LEU* 4.2 5.2 - - + -
32J TYR* 4.5 12.3 - - + -
33J TYR 3.5 6.7 - - - -
34J TRP* 3.5 30.7 - - + -
93J ALA* 1.3 72.6 - - - +
95J ALA* 1.3 60.8 + - - +
96J ARG* 3.7 15.6 + - - +
100J MET* 3.3 27.8 + - - -
101J ASP* 2.7 28.5 + - - -
102J VAL* 3.0 27.2 + - + +
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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