Contacts of the strand formed by residues 129 - 137 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A PHE* 3.7 16.2 - - + +
43A GLU 2.9 25.5 + - - +
44A LYS* 3.3 3.7 + - - +
126A ARG* 3.5 21.9 + - + +
127A PHE 2.9 14.4 + - - -
128A ASN* 1.3 77.2 + - - +
130A ALA* 1.3 61.4 + - - +
147A VAL* 3.6 34.5 - - + -
148A GLN 3.2 10.3 - - - +
149A ASP* 4.0 12.2 + - - +
156A TYR* 4.4 5.5 + - - +
500A FAD 3.5 5.0 - - - -
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LYS* 3.9 11.4 - - + -
65A GLU* 3.4 36.8 - - + +
128A ASN 4.2 1.0 + - - -
129A THR* 1.3 73.1 - - - +
131A VAL* 1.3 64.1 + - - +
132A ARG* 3.6 9.0 + - - +
147A VAL* 3.2 3.8 - - - -
148A GLN* 2.7 38.5 + - - +
150A HIS* 4.0 6.9 - - + +
500A FAD 3.7 7.4 - - - +
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.0 21.5 - - + -
42A PHE* 3.8 27.1 - - + -
130A ALA* 1.3 71.5 - - - +
132A ARG* 1.3 66.6 + - - +
133A HIS 4.2 0.7 - - - +
134A VAL* 4.0 20.0 - - + -
145A VAL* 4.3 6.5 - - + -
146A THR 3.9 8.7 - - - +
147A VAL* 4.0 7.6 - - + -
285A PHE* 3.9 29.9 - - + +
500A FAD 3.0 39.0 + - + +
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLU* 2.2 44.0 + - - -
130A ALA* 3.9 8.7 - - - +
131A VAL* 1.3 78.0 + - - +
133A HIS* 1.3 64.1 + - + +
146A THR* 2.8 26.3 + - + +
147A VAL 4.3 2.2 - - - -
148A GLN* 3.1 43.1 + - + +
150A HIS* 4.3 0.2 - - - -
155A ILE* 5.1 9.2 - - + +
284A PRO 4.2 3.3 - - - +
285A PHE* 3.2 19.7 - - - +
282D HIS* 4.5 7.7 - - - -
284D PRO* 3.5 39.3 + - - +
286D LEU 5.8 0.2 - - - -
287D ASN* 6.0 0.2 - - - +
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Residues in contact with HIS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A VAL 3.8 0.4 - - - -
132A ARG* 1.3 84.3 + - + +
134A VAL* 1.3 77.8 + - - +
135A GLU* 3.3 34.4 + - + -
144A THR 3.8 0.8 - - - +
145A VAL* 3.5 1.2 - - - +
146A THR* 2.9 42.3 + - + +
284A PRO 5.7 0.4 + - - -
285A PHE* 3.4 13.6 + - - +
286A LEU 5.1 0.2 - - - -
287A ASN* 3.4 35.6 + - - -
133D HIS* 3.0 44.6 - + + +
135D GLU* 5.0 0.2 - - - -
146D THR* 5.3 4.8 + - + +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.5 10.1 - - + -
131A VAL* 4.0 19.1 - - + -
133A HIS* 1.3 88.3 + - - +
135A GLU* 1.3 69.2 + - - +
143A PHE* 4.1 23.1 - - + -
144A THR 3.5 6.3 - - - +
145A VAL* 4.1 19.7 - - + -
163A VAL* 4.6 2.9 - - + -
285A PHE* 2.8 16.1 + - + +
286A LEU* 3.5 26.7 - - + -
287A ASN* 4.6 3.8 + - - +
290A LEU* 4.2 16.5 - - + +
315A PHE* 4.4 7.6 - - + -
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Residues in contact with GLU 135 (chain A).
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* 3.3 38.2 + - + +
134A VAL* 1.3 74.1 - - - +
136A PHE* 1.3 67.7 + - - +
137A ASN* 4.6 8.9 - - - +
143A PHE* 3.2 9.2 - - - +
144A THR* 2.8 42.8 + - + +
287A ASN* 4.3 12.9 + - - +
289A ASP* 5.9 0.2 - - - -
290A LEU* 4.9 1.3 - - - -
133D HIS* 5.0 0.3 - - - -
135D GLU* 4.0 13.3 - - - +
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Residues in contact with PHE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 1.3 79.9 - - - +
137A ASN* 1.3 68.7 + - - +
138A GLU* 3.9 24.2 + - - +
141A GLN* 3.7 60.3 - - - -
142A THR 3.5 11.4 - - - -
143A PHE* 3.6 33.8 - + + -
289A ASP* 4.4 16.5 + - - +
290A LEU* 4.7 4.4 - - + +
312A ASN* 3.4 27.4 - - - +
314A LYS* 4.4 10.3 - - + -
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Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 4.5 9.6 - - - +
136A PHE* 1.3 79.4 - - - +
138A GLU* 1.3 59.9 + - - +
139A ASP* 4.4 5.6 - - + +
140A SER* 3.7 13.0 + - - +
141A GLN* 2.9 30.1 + - - -
142A THR* 2.9 34.9 + - - -
143A PHE 4.2 0.4 - - - -
144A THR* 3.1 30.4 + - - +
159A ALA* 6.3 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