Contacts of the strand formed by residues 37 - 45 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TRP* 4.4 3.6 - - + -
26A ALA* 4.1 0.5 - - - +
27A TYR* 3.3 24.8 + - - +
33A LEU 3.8 12.6 - - - -
34A PHE* 3.1 31.6 + - + +
35A VAL 3.6 3.6 - - - +
36A GLY* 1.3 80.6 - - - +
38A VAL* 1.3 67.5 + - - +
106A VAL* 5.6 7.3 - - - +
145A ILE* 3.6 25.4 + - + +
146A LEU 3.1 18.4 - - - +
147A ASN* 3.0 28.5 + - - +
148A ASP* 3.8 3.8 - - - +
154A GLN* 4.2 12.6 + - - +
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Residues in contact with VAL 38 (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 TRP* 3.9 4.9 - - - -
16A ARG* 4.3 9.9 - - - +
24A VAL* 4.0 17.5 - - + -
25A LEU 3.3 13.0 - - - +
26A ALA* 3.9 15.5 - - + -
37A LYS* 1.3 79.5 - - - +
39A ILE* 1.3 59.8 + - - +
40A ARG 4.2 0.2 + - - -
144A LEU 3.4 0.7 - - - +
145A ILE* 3.3 6.2 - - - +
146A LEU* 2.8 53.6 + - + -
147A ASN 3.7 17.0 - - - +
148A ASP* 4.1 17.7 - - + -
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Residues in contact with ILE 39 (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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5A LEU* 5.2 1.8 - - + -
13A TRP* 3.5 36.5 - - + -
23A LEU 3.7 0.5 - - - +
24A VAL* 3.3 7.7 - - - +
25A LEU* 2.8 58.9 + - + +
38A VAL* 1.3 73.9 - - - +
40A ARG* 1.3 62.4 + - - +
41A ILE* 3.9 19.0 + - + -
108A VAL* 5.1 0.7 - - + -
110A VAL* 4.6 3.6 - - + -
114A PHE* 4.1 21.8 - - + -
143A ALA* 3.7 25.1 - - + -
144A LEU 3.2 10.3 - - - +
145A ILE* 4.4 11.0 - - + +
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Residues in contact with ARG 40 (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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22A ASN* 3.2 36.7 + - + +
23A LEU 3.7 2.5 - - - -
24A VAL* 3.8 21.1 - - + -
38A VAL 4.2 0.4 + - - -
39A ILE* 1.3 71.8 - - - +
41A ILE* 1.3 62.8 + - - +
42A GLN* 4.2 1.9 + - - +
82A GLU* 5.5 1.6 - - - +
85A GLU* 4.5 17.3 + - - +
143A ALA* 4.1 2.8 - - - +
144A LEU* 2.9 46.6 + - + +
146A LEU* 3.8 29.8 - - + +
407A ASP* 3.9 36.5 + - - +
408A LEU 4.4 4.8 + - - +
409A SER* 3.2 25.9 + - - -
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Residues in contact with ILE 41 (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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22A ASN* 3.4 5.2 - - - -
23A LEU* 2.8 42.9 + - + +
25A LEU* 3.6 27.8 - - + -
39A ILE* 3.9 25.6 - - + -
40A ARG* 1.3 77.9 - - - +
42A GLN* 1.3 70.5 + - - +
43A LYS 3.6 0.2 + - - -
114A PHE* 4.8 3.8 - - + -
115A LEU* 4.1 24.7 - - + -
118A VAL* 4.2 13.9 - - + -
136A VAL* 3.6 29.2 - - + -
137A ASP 5.1 3.1 - - - +
142A SER 5.8 1.8 - - - +
143A ALA* 4.6 7.6 - - + +
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Residues in contact with GLN 42 (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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21A ALA* 3.7 2.7 - - + +
22A ASN* 3.4 22.6 + - - +
40A ARG* 4.2 2.2 + - - +
41A ILE* 1.3 79.0 - - - +
43A LYS* 1.3 57.9 + - - +
81A LYS* 3.5 42.3 + - - +
82A GLU* 3.8 25.7 + - - +
85A GLU* 4.6 16.2 + - - +
136A VAL* 3.6 2.9 - - - -
137A ASP* 2.8 31.5 + - + +
140A HIS* 3.3 23.1 - - + +
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Residues in contact with LYS 43 (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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18A GLU* 2.9 23.0 + - - +
19A GLY 2.6 28.6 + - - -
20A GLY* 3.2 25.2 + - - +
21A ALA* 2.9 17.0 + - - +
22A ASN 3.6 16.2 - - - +
23A LEU* 4.2 18.2 - - + +
42A GLN* 1.3 80.1 - - - +
44A ALA* 1.3 60.6 + - - +
45A ARG* 3.7 8.2 + - + +
126A ARG* 4.1 12.2 - - - +
130A ARG* 4.1 6.7 + - - +
133A ALA* 6.2 1.2 - - - +
134A ALA* 3.8 22.6 - - + +
135A ASN 2.9 16.2 - - - +
136A VAL* 4.4 1.8 - - - +
137A ASP* 3.9 6.7 - - - +
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Residues in contact with ALA 44 (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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43A LYS 1.3 64.5 - - - -
45A ARG* 1.3 64.2 + - - +
46A ARG* 3.6 5.5 + - - +
134A ALA* 3.5 14.8 - - - +
135A ASN* 2.4 31.0 + - + +
136A VAL 4.1 3.8 - - - +
137A ASP* 3.6 33.0 - - + +
138A THR 5.2 0.2 - - - +
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Residues in contact with ARG 45 (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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20A GLY* 3.7 21.1 + - - +
21A ALA* 3.3 20.6 - - - +
43A LYS* 3.7 9.1 + - + +
44A ALA* 1.3 75.1 - - - +
46A ARG* 1.3 57.4 + - - +
47A ASN* 3.1 30.5 - - - +
48A ASP* 3.1 36.8 - - + +
133A ALA* 3.9 0.7 - - - -
134A ALA* 3.8 15.3 - - + -
415A ARG* 3.6 16.8 - - - +
500A IHP 3.0 44.6 + - - -
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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