Contacts of the strand formed by residues 118 - 124 (chain D) in PDB entry 5JCZ
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D VAL 3.2 12.6 + - - +
86D GLY* 3.3 1.4 - - - -
87D ALA 2.8 26.7 + - - -
116D ASN 4.3 3.6 - - - +
117D ILE* 1.3 72.7 - - - +
119D ILE* 1.3 66.1 + - - +
149D SER* 4.9 1.1 - - - +
168D ILE* 3.5 21.8 - - + +
171D GLU* 3.3 34.8 - - + +
172D ILE* 3.7 25.4 - - + -
175D ILE* 3.8 28.5 - - + -
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Residues in contact with ILE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ALA* 3.5 11.2 - - + +
89D LEU* 4.3 22.2 - - + -
106D LEU* 4.1 2.2 - - + -
109D LEU* 3.5 35.4 - - + -
110D ARG* 3.6 37.5 - - - +
117D ILE* 3.6 15.2 + - + +
118D VAL* 1.3 81.7 - - - +
120D MET* 1.3 64.9 + - - +
121D LEU 4.2 0.2 - - - -
147D GLY 4.8 0.8 - - - +
148D LEU* 3.6 28.9 - - + -
149D SER* 2.9 25.7 + - - -
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Residues in contact with MET 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ALA 3.0 8.1 + - - -
88D LEU* 3.5 19.1 - - + -
89D LEU 2.8 26.9 + - - -
119D ILE* 1.3 76.3 - - - +
121D LEU* 1.3 71.5 + - - +
122D VAL* 3.5 4.8 + - + +
149D SER* 3.4 25.8 - - - +
150D PHE 4.3 2.0 - - - +
151D ILE* 3.6 27.1 - - + -
164D ALA* 3.4 33.4 - - - +
167D THR* 3.7 28.5 - - + -
168D ILE* 3.9 14.5 - - + +
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D LEU* 3.4 23.3 - - + +
91D TYR* 3.7 29.8 - - + -
99D TYR* 4.5 3.1 - - + -
102D VAL* 4.0 25.4 - - + -
119D ILE* 4.2 0.8 - - - +
120D MET* 1.3 69.9 - - - +
122D VAL* 1.3 60.2 + - - +
123D GLY 4.1 0.2 - - - -
139D ALA* 3.5 28.3 - - + +
142D PHE* 4.2 16.2 - - + -
143D ALA* 4.2 8.3 - - + -
148D LEU* 4.3 13.9 - - + +
149D SER 2.6 17.2 + - - +
150D PHE* 3.3 13.8 - - + -
151D ILE 3.1 25.1 + - - +
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Residues in contact with VAL 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LEU* 4.2 15.7 - - + -
88D LEU* 4.0 24.7 - - + -
89D LEU 2.7 13.8 + - - +
90D VAL* 3.2 9.5 - - + -
91D TYR* 2.9 30.8 + - - -
120D MET* 3.8 23.8 - - + +
121D LEU* 1.3 76.8 - - - +
123D GLY* 1.3 61.6 + - - +
124D ASN 3.5 2.5 + - - +
151D ILE* 3.4 9.6 - - + +
153D THR* 3.3 35.9 - - + +
164D ALA* 5.0 2.0 - - + -
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Residues in contact with GLY 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D TYR* 3.4 31.8 + - - -
93D ILE* 3.6 10.5 - - - +
121D LEU 4.1 0.2 + - - -
122D VAL* 1.3 69.4 - - - +
124D ASN* 1.3 64.4 + - - +
126D SER 4.6 0.5 + - - -
150D PHE* 4.6 0.2 - - - -
151D ILE 3.0 13.4 + - - -
152D GLU* 3.2 10.7 - - - +
153D THR 2.8 23.5 + - - +
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Residues in contact with ASN 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D VAL 2.9 28.6 + - - +
23D GLY* 3.6 19.4 + - - -
27D LEU* 3.7 9.3 - - - +
90D VAL* 3.8 11.9 - - + -
91D TYR 2.9 12.9 + - - +
93D ILE* 3.2 23.2 + - - +
122D VAL 3.5 1.2 + - - -
123D GLY* 1.3 74.0 - - - +
125D LYS* 1.3 88.3 + - - +
153D THR* 3.0 22.6 + - - +
155D ALA* 3.3 25.4 + - - +
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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