Contacts of the strand formed by residues 124 - 130 (chain D) in PDB entry 2WZJ
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 THR 124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D ILE* 3.6 28.3 - - + -
84D ILE 3.3 13.0 - - - +
85D ASP* 4.7 3.5 + - - +
86D LYS* 4.1 5.2 + - - -
119D ILE 4.2 0.2 - - - +
120D GLU* 3.8 1.4 - - - -
121D THR* 2.9 40.9 + - - +
122D GLU 3.6 0.8 - - - -
123D LYS* 1.3 87.4 + - - +
125D LEU* 1.3 64.4 + - - +
126D TYR* 3.7 26.3 + - + +
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Residues in contact with LEU 125 (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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82D ARG 3.6 2.1 - - - +
83D ILE* 3.7 0.9 - - - -
84D ILE* 2.8 51.0 + - + +
86D LYS* 4.1 13.0 - - + -
97D LEU* 3.8 31.0 - - + -
98D PHE* 4.4 16.2 - - + -
101D VAL* 4.6 2.9 - - + -
118D VAL* 3.7 25.1 - - + -
119D ILE 3.7 2.5 - - - +
120D GLU* 3.7 31.2 - - + -
124D THR* 1.3 75.0 - - - +
126D TYR* 1.3 62.1 + - - +
127D LEU* 3.7 26.8 + - + -
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Residues in contact with TYR 126 (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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50D ILE* 3.4 48.4 - - + +
55D LEU* 5.6 1.3 - - + -
81D VAL* 3.9 15.9 - - + -
82D ARG 3.4 4.3 - - - -
83D ILE* 3.8 39.4 - - + +
117D GLU 3.7 0.9 - - - +
118D VAL* 3.6 6.1 - - - +
119D ILE* 2.7 59.6 + - + +
121D THR* 4.2 11.8 - - + +
124D THR* 3.7 28.7 + - + +
125D LEU* 1.3 74.7 - - - +
127D LEU* 1.3 64.2 + - - +
128D VAL* 3.9 1.1 + - + -
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Residues in contact with LEU 127 (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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80D ALA 3.4 2.6 - - - +
81D VAL* 3.3 4.3 - - - -
82D ARG* 2.9 43.9 + - + +
84D ILE* 3.9 26.0 - - + -
97D LEU* 5.0 0.2 - - + -
101D VAL* 3.7 34.3 - - + -
104D MET* 3.8 16.6 - - + -
115D LEU* 3.9 11.4 - - + -
117D GLU 3.9 1.6 - - - -
118D VAL* 4.0 20.6 - - + -
125D LEU* 3.7 16.8 - - + -
126D TYR* 1.3 76.9 - - - +
128D VAL* 1.3 60.9 + - - +
129D MET* 3.8 10.5 + - + +
196D PHE* 4.3 13.2 - - + -
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Residues in contact with VAL 128 (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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53D TYR* 3.6 48.7 - - + +
79D VAL* 3.9 22.4 - - + -
80D ALA 3.6 3.1 - - - +
81D VAL* 4.3 17.9 - - + -
115D LEU* 3.6 3.4 - - - +
116D PHE* 2.6 40.5 + - + -
117D GLU* 2.9 29.2 + - + +
119D ILE* 4.7 10.3 - - + -
126D TYR 4.7 0.9 - - - +
127D LEU* 1.3 72.5 - - - +
129D MET* 1.3 56.6 + - - +
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Residues in contact with MET 129 (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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79D VAL* 3.7 5.0 - - - +
80D ALA* 2.8 44.7 + - + +
82D ARG* 4.9 2.5 - - - -
104D MET* 3.7 23.3 - - + +
113D VAL* 4.9 14.6 - - + -
114D LYS 3.2 15.5 - - - +
115D LEU* 3.6 25.1 - - + -
116D PHE* 3.7 7.2 - - - -
127D LEU* 4.0 18.6 - - + +
128D VAL* 1.3 73.1 - - - +
130D GLU* 1.3 75.3 + - - +
196D PHE* 6.1 0.4 - - + -
198D ASN* 3.5 33.4 - - - +
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Residues in contact with GLU 130 (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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80D ALA* 4.1 4.2 - - - +
112D ILE 3.5 5.0 - - - +
113D VAL* 3.3 21.4 - - + +
114D LYS* 2.7 47.1 + - + +
116D PHE* 3.4 29.6 - - + -
129D MET* 1.3 82.1 - - - +
131D TYR* 1.3 62.9 + - - +
132D ALA 4.1 1.4 + - - -
190D LYS* 2.8 38.7 + - + +
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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