Contacts of the strand formed by residues 86 - 92 (chain S) in PDB entry 4UJ3
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 GLY 86 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13S LYS 3.4 2.8 + - - +
14S VAL* 3.2 13.5 - - - -
15S VAL* 2.9 25.5 + - - +
84S ALA* 4.1 0.5 - - - +
85S VAL* 1.3 84.5 - - - +
87S ALA* 1.3 61.4 + - - +
117S ILE* 3.2 6.7 - - - +
118S VAL 3.1 10.8 - - - -
168S ILE* 4.6 0.9 - - - -
172S ILE* 3.8 14.8 - - - -
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Residues in contact with ALA 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S VAL* 3.9 0.6 - - - +
15S VAL* 3.2 21.3 - - + +
17S ILE* 4.8 4.5 - - + -
86S GLY* 1.3 75.6 - - - +
88S LEU* 1.3 61.1 + - - +
89S LEU 3.6 1.4 + - - -
109S LEU* 3.9 30.5 - - + -
117S ILE* 4.1 9.4 - - + -
118S VAL 2.8 10.1 + - - +
119S ILE* 3.5 4.1 - - + +
120S MET 3.0 26.0 + - - -
168S ILE* 3.7 6.7 - - - +
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Residues in contact with LEU 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S VAL* 4.3 8.1 - - + -
15S VAL 2.9 9.3 + - - -
16S LEU* 3.4 29.4 - - + -
17S ILE* 2.9 30.0 + - - +
27S LEU* 5.7 3.8 - - + -
87S ALA* 1.3 69.2 - - - +
89S LEU* 1.3 61.1 + - - +
90S VAL* 3.5 9.9 + - + +
120S MET* 3.2 39.5 - - + -
122S VAL* 4.2 6.7 - - + -
164S ALA* 5.7 1.6 - - + -
165S PHE* 3.5 37.0 - - + -
168S ILE* 3.2 25.8 - - + -
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Residues in contact with LEU 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S ILE* 3.3 23.3 - - + -
18S GLY* 4.2 2.5 - - - -
87S ALA 3.6 1.8 + - - -
88S LEU* 1.3 69.9 - - - +
90S VAL* 1.3 67.5 + - - +
102S VAL* 3.6 50.3 - - + +
105S TRP* 3.7 20.9 - - + -
106S LEU* 3.7 32.1 - - + +
109S LEU* 4.9 1.1 - - + -
119S ILE* 4.7 8.7 - - + -
120S MET 2.9 15.1 + - - +
121S LEU* 3.6 12.1 - - + +
122S VAL 2.9 24.8 + - - +
148S LEU* 5.8 1.6 - - + -
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Residues in contact with VAL 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S LEU* 4.6 3.6 - - + -
17S ILE 2.6 13.9 + - - +
18S GLY* 3.3 19.4 - - - -
19S ASP 3.8 1.2 + - - -
22S VAL* 3.4 31.2 - - + +
24S LYS* 4.0 9.0 - - + -
27S LEU* 3.8 26.0 - - + -
88S LEU* 3.6 22.2 - - + +
89S LEU* 1.3 78.0 - - - +
91S TYR* 1.3 72.3 + - - +
98S THR 4.9 0.7 - - - +
102S VAL* 5.4 0.2 - - - +
105S TRP* 5.5 0.2 - - - -
122S VAL* 2.8 15.0 - - + +
124S ASN* 3.9 17.3 - - + -
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Residues in contact with TYR 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22S VAL* 3.5 11.9 - - - -
90S VAL* 1.3 74.6 - - - +
92S ASP* 1.3 66.3 + - - +
93S ILE* 4.4 12.6 - - + +
98S THR 3.2 23.3 - - - +
99S TYR* 3.2 43.1 - + + -
102S VAL* 4.0 6.7 - - + -
121S LEU* 4.0 24.5 - - + -
122S VAL 2.6 32.2 + - - +
123S GLY* 3.0 21.9 + - - -
124S ASN* 3.4 29.1 + - - +
134S VAL* 3.4 17.8 - - + +
139S ALA* 3.0 28.5 - - + +
150S PHE* 3.8 7.8 - + - -
152S GLU* 4.6 2.4 + - - -
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Residues in contact with ASP 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22S VAL* 3.5 14.3 - - - +
91S TYR* 1.3 76.2 - - - +
93S ILE* 1.3 58.0 + - - +
94S ALA* 2.9 20.4 + - - +
95S LYS* 2.8 55.9 + - + +
98S THR* 2.9 24.0 + - + +
124S ASN 4.1 2.0 - - - -
125S LYS* 2.6 48.9 + - - +
134S VAL* 4.8 0.7 - - - +
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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