Contacts of the strand formed by residues 2 - 7 (chain D) in PDB entry 2B0U
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 ASN 2 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D GLY* 1.3 89.2 - - - +
3D CYS* 1.3 60.0 + - - +
4D TRP* 3.0 28.7 - - - +
16D LEU* 3.9 18.2 - - + +
18D LYS 4.4 3.8 - - - -
19D THR* 3.5 19.0 + - - -
36D TRP* 3.2 5.7 - - - +
37D THR* 2.5 43.3 + - + +
39D GLU 3.5 15.5 + - - -
40D ASP* 3.2 8.7 - - - +
41D VAL* 3.7 30.1 + - - +
46D LEU* 4.6 0.2 - - - +
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Residues in contact with CYS 3 (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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2D ASN* 1.3 72.9 - - - +
4D TRP* 1.3 59.5 + - - +
16D LEU* 3.7 8.0 - - - +
17D TYR* 3.2 40.1 + - + -
18D LYS 4.0 7.6 + - - +
21D LEU* 4.0 18.0 - - + +
26D CYS* 2.0 57.0 - - + -
34D THR* 3.7 16.6 - - - -
35D SER 3.5 3.1 - - - -
36D TRP* 4.2 0.2 - - - -
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Residues in contact with TRP 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 3.4 26.0 - - + -
2D ASN* 3.0 42.5 + - + +
3D CYS* 1.3 74.8 - - - +
5D LEU* 1.3 61.6 + - - +
6D ARG 3.8 2.0 - - - +
13D CYS* 3.1 61.2 - - + -
14D GLN* 3.6 14.8 - - - +
15D VAL 3.4 7.4 - - - -
16D LEU* 3.9 14.1 - - + -
17D TYR* 3.7 3.7 - - - -
34D THR* 3.2 12.1 - - - +
35D SER* 2.7 26.9 + - - +
37D THR* 3.0 27.3 - - + -
46D LEU* 3.4 34.5 - - + -
49D TRP* 5.0 0.2 - + - -
50D MET* 5.8 3.8 - - - -
56D ALA* 3.6 18.8 - - + -
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Residues in contact with LEU 5 (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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1A GLY 5.1 2.9 - - - +
2A LEU* 2.6 39.7 - - + -
4D TRP* 1.3 73.2 - - - +
6D ARG* 1.3 63.4 + - + +
14D GLN 3.2 0.4 + - - -
15D VAL* 3.0 22.2 + - + +
17D TYR* 2.4 45.8 - - + +
31D ARG* 3.2 35.0 - - - +
33D SER* 3.4 20.6 - - - -
34D THR* 3.4 19.3 - - - +
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Residues in contact with ARG 6 (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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1A GLY* 4.2 35.8 + - - +
52A SER 3.9 18.6 + - - -
53A GLY* 5.2 5.3 + - - -
4D TRP* 3.8 1.0 - - - +
5D LEU* 1.3 81.5 - - + +
7D GLN* 1.3 84.5 + - - +
8D ALA* 4.2 0.7 - - - +
12D ARG 3.5 3.1 - - - +
13D CYS* 3.5 6.1 - - - +
14D GLN* 3.2 54.2 + - - +
15D VAL* 4.1 14.1 - - + +
33D SER* 4.4 9.6 + - - +
35D SER* 4.3 5.0 + - - +
59D CYS* 4.1 2.1 - - - -
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Residues in contact with GLN 7 (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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6D ARG* 1.3 87.0 - - - +
8D ALA* 1.3 62.4 + - - +
11D GLY* 4.3 16.8 - - - +
12D ARG 3.8 2.7 - - - +
14D GLN* 4.7 0.4 - - - -
33D SER* 4.5 10.8 + - - +
35D SER* 3.4 19.2 + - - +
59D CYS* 3.8 14.4 - - + +
61D PRO* 3.2 40.6 - - - +
84D LYS* 4.1 27.1 + - - +
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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