Contacts of the strand formed by residues 37 - 45 (chain B) in PDB entry 2XAR
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 LYS 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TRP* 4.4 4.0 - - + -
26B ALA* 4.1 0.9 - - - +
27B TYR* 3.3 24.9 + - - +
33B LEU 3.8 13.7 - - - +
34B PHE* 3.0 32.4 + - + +
35B VAL 3.7 3.4 - - - +
36B GLY* 1.3 79.4 - - - +
38B VAL* 1.3 67.4 + - - +
106B VAL* 6.2 1.8 - - - +
145B ILE* 3.9 21.6 - - + +
146B LEU 3.6 15.9 - - - +
147B ASN* 3.2 22.6 - - - +
148B ASP* 4.2 3.5 - - - +
154B GLN* 3.5 24.2 + - - +
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Residues in contact with VAL 38 (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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13B TRP* 3.9 4.7 - - - -
16B ARG* 4.3 9.0 - - - +
24B VAL* 4.1 17.7 - - + -
25B LEU 3.3 13.5 - - - +
26B ALA* 3.9 16.6 - - + -
37B LYS* 1.3 79.5 - - - +
39B ILE* 1.3 60.0 + - - +
144B LEU 3.7 0.2 - - - +
145B ILE* 3.4 7.4 - - - +
146B LEU* 3.2 44.8 + - + +
147B ASN 3.7 20.4 - - - +
148B ASP* 4.0 19.5 - - - +
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Residues in contact with ILE 39 (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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5B LEU* 5.2 2.0 - - + -
13B TRP* 3.5 36.0 - - + -
23B LEU 3.8 0.5 - - - +
24B VAL* 3.3 8.3 - - - +
25B LEU* 2.8 60.8 + - + +
38B VAL* 1.3 73.5 - - - +
40B ARG* 1.3 61.9 + - - +
41B ILE* 3.9 18.7 + - + +
108B VAL* 4.9 0.7 - - + -
110B VAL* 4.5 4.0 - - + -
114B PHE* 4.1 22.2 - - + -
143B ALA* 3.6 24.9 - - + -
144B LEU 3.2 10.1 - - - +
145B ILE* 4.3 12.1 - - + -
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Residues in contact with ARG 40 (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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22B ASN* 3.4 33.9 + - - +
23B LEU 3.7 2.2 - - - -
24B VAL* 3.8 21.5 - - + -
38B VAL 4.2 0.4 - - - -
39B ILE* 1.3 73.7 - - - +
41B ILE* 1.3 61.2 + - - +
42B GLN* 4.1 2.1 + - - +
82B GLU* 5.6 1.2 - - - +
85B GLU* 4.8 10.9 + - - +
143B ALA* 4.1 1.6 - - - +
144B LEU* 2.7 53.1 + - + +
146B LEU* 3.4 32.5 - - + +
407B ASP* 3.6 37.8 + - - +
408B LEU 3.9 8.7 + - - +
409B SER* 3.3 25.3 + - - -
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Residues in contact with ILE 41 (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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22B ASN* 3.4 5.6 + - - -
23B LEU* 2.9 41.9 + - + +
25B LEU* 3.7 28.7 - - + -
39B ILE* 3.9 25.8 - - + -
40B ARG* 1.3 77.9 - - - +
42B GLN* 1.3 75.5 + - - +
43B LYS* 3.6 0.3 + - - +
114B PHE* 4.7 3.4 - - + -
115B LEU* 4.1 26.0 - - + -
118B VAL* 4.4 10.3 - - + -
136B VAL* 3.8 25.4 - - + -
137B ASP 5.2 2.5 - - - +
142B SER 5.7 2.5 - - - +
143B ALA* 4.4 8.1 - - + +
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Residues in contact with GLN 42 (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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21B ALA* 4.5 2.9 - - + +
22B ASN* 3.5 21.0 - - - +
40B ARG* 4.1 2.5 + - - +
41B ILE* 1.3 80.9 - - - +
43B LYS* 1.3 64.7 + - - +
81B LYS* 3.4 52.2 + - - +
82B GLU* 3.7 23.8 + - + +
85B GLU* 4.1 23.9 + - - +
136B VAL* 4.1 0.3 - - - -
137B ASP* 3.3 23.1 + - - +
140B HIS* 3.8 12.5 + - + -
144B LEU* 5.9 1.4 - - - +
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Residues in contact with LYS 43 (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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18B GLU* 2.9 23.4 + - - +
19B GLY 2.7 28.7 + - - -
20B GLY* 3.1 25.0 + - - +
21B ALA* 2.9 18.1 + - - +
22B ASN 3.6 15.0 - - - +
23B LEU* 4.2 18.4 - - + +
42B GLN* 1.3 79.2 - - - +
44B ALA* 1.3 60.7 + - - +
45B ARG* 3.7 9.3 + - + +
126B ARG* 4.4 9.1 - - - +
130B ARG* 4.2 7.5 + - - +
134B ALA* 4.1 22.3 - - + +
135B ASN 3.4 15.5 - - - +
136B VAL* 4.4 1.8 - - + +
137B ASP* 4.2 4.3 - - - +
140B HIS* 6.1 0.2 - - - -
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Residues in contact with ALA 44 (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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43B LYS* 1.3 69.8 - - - +
45B ARG* 1.3 64.3 + - - +
46B ARG* 3.5 5.9 + - - +
134B ALA* 3.5 17.1 - - - +
135B ASN 2.9 12.8 + - - +
136B VAL 4.5 1.3 - - - +
137B ASP* 3.5 40.0 - - + +
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Residues in contact with ARG 45 (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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20B GLY* 3.7 19.3 + - - +
21B ALA* 3.3 16.7 - - - +
43B LYS* 3.7 9.1 + - + +
44B ALA* 1.3 72.9 - - - +
46B ARG* 1.3 59.2 + - - +
47B ASN* 3.2 25.3 + - - +
48B ASP* 3.3 46.4 + - - +
49B LYS* 4.2 1.6 + - - -
133B ALA 4.4 1.1 - - - +
134B ALA* 4.1 13.0 - - + -
415B ARG* 3.2 18.8 - - - +
500B IHP 2.7 54.9 + - - -
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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