Contacts of the strand formed by residues 118 - 124 (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 VAL 118 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85S VAL 2.8 10.8 + - - +
86S GLY* 3.1 1.7 - - - -
87S ALA 2.8 26.5 + - - +
116S ASN 4.3 6.7 - - - +
117S ILE* 1.3 70.9 - - - +
119S ILE* 1.3 65.2 + - - +
149S SER* 4.6 0.9 - - - +
168S ILE* 3.8 20.9 - - + +
171S GLU* 3.4 36.1 - - + +
172S ILE* 3.4 43.1 - - + +
175S ILE* 4.6 12.1 - - + -
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Residues in contact with ILE 119 (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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87S ALA* 3.5 8.5 - - + +
89S LEU* 4.7 8.3 - - + -
106S LEU* 4.0 16.8 - - + -
109S LEU* 3.2 40.8 - - + -
110S ARG* 4.8 11.0 - - + -
117S ILE* 3.3 27.2 + - + +
118S VAL* 1.3 77.6 - - - +
120S MET* 1.3 68.6 + - - +
147S GLY 4.5 2.0 - - - +
148S LEU* 3.4 31.5 - - + -
149S SER* 3.4 22.0 + - - -
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Residues in contact with MET 120 (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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87S ALA 3.0 7.7 + - - -
88S LEU* 3.2 36.3 - - + -
89S LEU* 2.9 30.0 + - - +
119S ILE* 1.3 77.2 - - - +
121S LEU* 1.3 67.9 + - - +
122S VAL* 3.7 11.1 + - + +
149S SER* 3.4 29.6 - - - +
150S PHE 4.3 1.6 - - - +
151S ILE* 3.7 13.2 - - + -
164S ALA* 3.1 50.9 - - + +
167S THR* 4.5 9.6 - - - -
168S ILE* 3.8 16.3 - - + +
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Residues in contact with LEU 121 (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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89S LEU* 3.6 20.0 - - + +
91S TYR* 4.0 16.2 - - + -
99S TYR* 5.2 3.8 - - + -
102S VAL* 3.7 36.3 - - + -
119S ILE 4.4 0.2 + - - -
120S MET* 1.3 72.5 - - - +
122S VAL* 1.3 62.9 + - - +
139S ALA* 4.0 15.9 - - + +
142S PHE* 4.4 14.8 - - + -
143S ALA* 3.9 22.4 - - + -
148S LEU* 4.6 10.6 - - + +
149S SER 3.0 15.2 + - - +
150S PHE* 3.6 16.6 - - + -
151S ILE 3.3 26.2 + - - +
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Residues in contact with VAL 122 (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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27S LEU* 4.3 14.1 - - + -
88S LEU* 4.2 9.9 - - + -
89S LEU 2.9 5.8 + - - +
90S VAL* 2.8 24.4 - - + +
91S TYR* 2.6 36.0 + - - -
120S MET* 3.7 34.5 - - + +
121S LEU* 1.3 79.4 - - - +
123S GLY* 1.3 60.8 + - - +
124S ASN* 3.5 2.7 - - + +
151S ILE* 3.7 3.8 - - + +
153S THR* 3.1 36.6 - - + +
164S ALA* 5.0 1.8 - - + -
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Residues in contact with GLY 123 (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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91S TYR* 3.0 19.4 - - - -
93S ILE* 3.3 16.7 - - - +
121S LEU 4.6 0.2 - - - -
122S VAL* 1.3 75.8 + - - -
124S ASN* 1.3 55.0 + - - +
126S SER* 4.8 0.2 - - - -
150S PHE* 5.0 0.7 - - - -
151S ILE 3.3 13.5 - - - -
152S GLU* 3.0 9.5 - - - +
153S THR 2.1 37.6 + - - +
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Residues in contact with ASN 124 (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 2.7 28.8 + - - +
23S GLY* 3.6 9.7 + - - -
27S LEU* 3.8 9.9 - - - +
90S VAL* 3.9 11.4 - - + -
91S TYR 3.4 8.0 + - - +
93S ILE* 2.9 28.2 + - - +
122S VAL* 4.4 0.9 - - + -
123S GLY* 1.3 78.8 - - - +
125S LYS* 1.3 82.4 + - - +
126S SER 3.3 0.7 - - - -
153S THR* 3.0 20.0 + - - +
155S ALA 3.3 18.5 + - - -
200S GNP 3.5 22.6 + - - -
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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