Contacts of the strand formed by residues 129 - 137 (chain D) in PDB entry 2XLR
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 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D PHE* 3.7 17.0 - - + +
43D GLU 2.7 30.3 + - - +
44D LYS* 3.3 2.5 + - - +
126D ARG* 3.6 22.4 + - + +
127D PHE 3.0 12.3 + - - -
128D ASN* 1.3 72.7 + - - +
130D ALA* 1.3 60.2 + - - +
131D VAL 3.8 0.2 + - - -
147D VAL* 3.6 35.0 - - + -
148D GLN 3.4 9.0 - - - +
149D ASP* 3.9 13.9 + - - +
156D TYR* 4.4 4.9 + - - +
500D FAD 3.5 5.2 - - - -
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Residues in contact with ALA 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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44D LYS* 4.0 11.0 - - + +
65D GLU* 3.3 37.9 - - + +
128D ASN 4.2 1.0 - - - -
129D THR* 1.3 72.6 - - - +
131D VAL* 1.3 64.9 + - - +
132D ARG* 4.0 8.2 - - - +
147D VAL* 3.2 5.1 - - - +
148D GLN* 2.8 37.6 + - + +
150D HIS* 4.1 6.8 - - + +
500D FAD 3.7 7.2 - - - +
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Residues in contact with VAL 131 (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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13D LEU* 4.1 21.5 - - + -
42D PHE* 3.8 29.2 - - + -
130D ALA* 1.3 72.3 - - - +
132D ARG* 1.3 68.3 + - - +
133D HIS 4.1 2.5 - - - +
134D VAL* 4.1 16.6 - - + -
145D VAL* 4.3 4.3 - - + -
146D THR 4.0 6.5 - - - +
147D VAL* 4.2 4.3 - - + -
285D PHE* 3.9 35.5 - - + +
500D FAD 2.9 40.7 + - + +
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Residues in contact with ARG 132 (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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282A HIS* 4.5 7.7 - - - -
284A PRO* 3.4 39.1 + - - +
286A LEU 5.9 0.2 - - - -
65D GLU* 2.2 44.8 + - - -
130D ALA* 4.0 8.1 - - - +
131D VAL* 1.3 82.5 + - - +
133D HIS* 1.3 64.0 + - + +
146D THR* 2.8 28.2 + - + +
147D VAL 4.3 2.0 - - - -
148D GLN* 3.2 42.4 + - + +
150D HIS* 4.4 0.2 - - - -
155D ILE* 5.1 9.6 - - + +
284D PRO 4.3 2.8 - - - +
285D PHE* 3.2 19.5 - - - +
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Residues in contact with HIS 133 (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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133A HIS* 3.0 43.5 - + + +
135A GLU* 5.0 0.2 - - - -
146A THR* 5.4 4.4 + - + +
131D VAL 3.9 0.4 - - - -
132D ARG* 1.3 84.1 - - + +
134D VAL* 1.3 78.6 + - - +
135D GLU* 3.4 33.8 + - + +
144D THR 3.7 1.4 - - - +
145D VAL* 3.4 1.4 - - - +
146D THR* 2.9 42.3 + - + +
285D PHE* 3.3 13.9 + - - +
287D ASN* 3.4 37.5 + - - -
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Residues in contact with VAL 134 (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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13D LEU* 4.6 10.5 - - + -
131D VAL* 4.1 18.6 - - + -
133D HIS* 1.3 90.0 + - - +
135D GLU* 1.3 63.6 + - - +
143D PHE* 4.0 24.2 - - + -
144D THR 3.4 6.1 - - - +
145D VAL* 4.2 20.9 - - + -
163D VAL* 4.5 2.7 - - + -
285D PHE* 2.8 12.0 + - + +
286D LEU* 3.6 24.1 - - + +
287D ASN* 4.7 5.2 + - - +
290D LEU* 4.1 17.0 - - + +
315D PHE* 4.3 7.4 - - + -
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Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A HIS* 5.0 0.5 - - - -
135A GLU* 4.0 13.7 - - - +
133D HIS* 3.4 37.5 + - + +
134D VAL* 1.3 73.4 - - - +
136D PHE* 1.3 63.8 + - - +
137D ASN* 4.4 10.1 + - - +
143D PHE* 3.2 7.4 - - - -
144D THR* 2.8 41.6 + - - +
287D ASN* 4.2 13.7 + - - +
290D LEU* 4.8 2.2 - - - -
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Residues in contact with PHE 136 (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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135D GLU* 1.3 78.5 + - - +
137D ASN* 1.3 67.7 + - - +
138D GLU* 3.9 24.3 + - - +
141D GLN* 3.6 61.9 - - - -
142D THR 3.4 11.2 - - - -
143D PHE* 3.6 35.7 - + + -
289D ASP* 4.5 16.9 + - - +
290D LEU* 4.5 5.9 - - + +
312D ASN* 3.4 28.7 - - - +
314D LYS* 4.4 8.1 - - + -
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Residues in contact with ASN 137 (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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135D GLU* 4.5 10.2 - - - +
136D PHE* 1.3 78.9 - - - +
138D GLU* 1.3 60.4 + - - +
139D ASP* 4.5 5.6 - - + +
140D SER* 3.7 13.0 + - - +
141D GLN* 2.9 31.4 + - - -
142D THR* 2.9 34.9 + - - -
143D PHE 4.3 0.2 - - - -
144D THR* 3.1 29.0 + - - +
159D ALA* 6.3 0.4 - - - +
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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