Contacts of the strand formed by residues 115 - 121 (chain B) in PDB entry 4XJO
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 LEU 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B VAL* 3.4 30.0 + - - +
111B THR* 3.9 11.9 - - - +
112B PRO* 3.5 27.0 + - + +
113B ALA 3.4 1.7 - - - +
114B GLY* 1.3 74.5 - - - +
116B ASP* 1.3 61.1 + - - +
117B THR 3.7 2.0 - - - -
276B PRO* 3.6 20.6 - - + +
277B ASP 3.6 26.2 - - - +
278B ILE* 4.2 2.9 - - - +
279B MET* 3.6 36.1 - - + +
296B LEU* 3.9 29.3 - - + +
297B CYS* 3.9 5.4 - - - -
298B THR* 4.2 1.8 - - + +
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Residues in contact with ASP 116 (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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19A ALA 3.6 2.4 - - - +
20A HIS* 2.7 36.0 + - + +
108B VAL* 3.6 16.0 - - - +
114B GLY* 3.2 21.9 + - - +
115B LEU* 1.3 78.4 - - - +
117B THR* 1.3 68.2 + - + +
297B CYS 3.1 4.9 + - - -
299B ALA* 4.0 26.7 - - + +
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Residues in contact with THR 117 (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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19A ALA 4.0 13.0 - - - +
20A HIS 3.3 7.6 - - - -
22A TRP* 3.0 25.6 + - - -
28A ILE* 4.1 14.4 - - + -
115B LEU 3.7 0.4 - - - -
116B ASP* 1.3 89.2 - - + +
118B VAL* 1.3 64.0 + - - +
296B LEU* 3.1 28.6 - - - +
297B CYS* 3.1 23.9 + - - +
298B THR 4.8 1.3 - - - +
299B ALA* 5.0 3.8 - - + -
302B ALA* 3.9 20.4 - - + -
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Residues in contact with VAL 118 (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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20A HIS 2.7 14.8 + - - +
21A LEU* 3.8 7.1 - - - +
22A TRP* 3.1 25.3 + - - +
104B ALA* 4.0 18.6 - - + +
107B LEU* 4.3 6.7 - - + -
108B VAL* 3.8 24.2 - - + -
117B THR* 1.3 80.8 - - - +
119B PHE* 1.3 60.3 + - - +
120B PHE* 3.7 37.5 + - + -
294B ALA* 4.0 15.3 - - + -
295B THR 3.7 3.1 - - - +
296B LEU* 3.8 15.0 - - + -
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Residues in contact with PHE 119 (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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22A TRP* 3.5 28.0 - + + -
23A HIS 4.4 3.1 - - - -
118B VAL* 1.3 71.8 - - - +
120B PHE* 1.3 79.3 + - - +
121B SER* 3.8 2.5 + - - -
130B VAL* 3.8 28.5 - - + -
134B MET* 3.9 9.0 - - + -
294B ALA* 3.3 1.9 - - - -
295B THR* 2.8 42.8 + - - +
313B LEU* 3.5 29.6 - - + -
315B HIS* 3.5 41.7 - - + -
317B PRO* 3.8 15.7 - - + -
320B MET* 3.6 14.8 - - + -
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Residues in contact with PHE 120 (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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21A LEU* 3.6 29.2 - - + -
92B PHE* 5.4 1.1 - + - -
100B ALA* 4.0 14.1 - - - -
103B LEU* 3.5 42.8 - - + -
104B ALA 4.1 4.3 - - - -
107B LEU* 4.0 10.1 - - + -
118B VAL* 3.7 21.0 + - + -
119B PHE* 1.3 83.3 - - - +
121B SER* 1.3 61.0 + - - +
285B LEU* 5.0 1.1 - - + -
292B LEU* 4.4 13.7 - - + -
293B ALA 3.6 13.9 - - - +
294B ALA* 3.9 5.6 - - + -
317B PRO* 4.0 1.0 - - - +
320B MET* 3.3 26.5 - - + +
321B ALA* 3.6 40.2 - - + +
326B CYS* 4.5 2.0 - - - -
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Residues in contact with SER 121 (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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119B PHE* 3.8 9.3 + - - -
120B PHE* 1.3 75.4 - - - +
122B ASP* 1.3 68.3 + - - +
123B SER 3.6 16.0 + - - -
126B VAL* 3.6 21.5 - - - -
127B SER* 3.6 19.7 + - - -
130B VAL* 4.9 0.4 - - - -
292B LEU* 3.4 11.8 - - - +
293B ALA* 2.9 28.7 + - - +
295B THR* 5.1 0.2 + - - -
317B PRO* 4.0 13.9 - - - -
320B MET* 5.3 1.1 - - - +
321B ALA 5.9 0.2 - - - -
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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