Contacts of the strand formed by residues 36 - 40 (chain D) in PDB entry 3UDB
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 ARG 36 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU 4.5 4.8 - - - +
13D PRO* 2.6 34.1 + - - +
14D ILE 4.2 5.7 - - - -
15D MET* 4.3 10.9 - - - +
23D LEU* 3.4 34.6 - - + +
25D LYS 3.7 2.9 - - - -
26D ASP* 2.4 58.0 + - - +
35D ALA* 1.3 77.5 - - - +
37D LEU* 1.3 64.6 + - - +
38D MET* 3.2 28.6 + - - +
48D ALA* 3.6 1.0 - - - -
49D VAL* 2.9 33.7 + - + +
51D TYR* 3.3 36.3 + - + -
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C CYS 5.2 0.9 - - - +
109C ALA 4.5 2.0 - - - +
110C GLY* 3.9 28.0 - - - +
23D LEU* 3.6 3.1 - - - +
24D VAL* 2.9 34.2 + - + -
25D LYS 2.8 15.2 + - - +
27D ILE* 3.9 26.7 - - + +
32D PHE* 6.1 1.1 - - + -
35D ALA* 5.5 2.7 - - + -
36D ARG* 1.3 78.2 - - - +
38D MET* 1.3 64.7 + - - +
46D LEU* 4.9 4.5 - - + -
47D VAL 3.5 4.0 - - - +
48D ALA* 4.2 11.2 - - + -
96D TYR* 4.0 53.2 - - + +
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Residues in contact with MET 38 (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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15D MET* 3.9 16.2 - - + -
16D HIS* 4.1 11.9 - - + +
21D TYR* 3.5 42.4 - - + -
22D GLU 3.4 11.2 - - - +
23D LEU* 4.3 4.9 - - - -
24D VAL* 3.7 6.5 - - - -
36D ARG* 3.2 30.7 + - - +
37D LEU* 1.3 79.1 - - - +
39D ARG* 1.3 59.9 + - - +
40D ASP 4.0 0.2 - - - -
46D LEU* 3.4 4.9 - - - +
47D VAL* 2.8 41.3 + - + +
49D VAL* 3.8 22.0 - - + -
51D TYR* 3.5 17.9 - - - +
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Residues in contact with ARG 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D TYR* 3.4 2.7 - - - -
22D GLU* 2.5 85.6 + - - +
24D VAL* 3.6 11.6 - - + +
38D MET* 1.3 73.4 - - - +
40D ASP* 1.3 65.0 + - - +
41D LYS* 3.3 35.2 + - - +
44D ASN* 3.2 37.8 + - - +
45D GLU 3.6 15.0 - - - +
46D LEU* 4.5 5.6 - - + +
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Residues in contact with ASP 40 (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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20D ARG* 3.8 10.8 + - - +
21D TYR* 3.3 34.6 + - + +
38D MET 4.0 1.4 + - - -
39D ARG* 1.3 71.5 - - - +
41D LYS* 1.3 63.0 + - - +
42D GLN* 2.3 32.7 + - - +
43D ALA* 3.6 10.3 - - - +
44D ASN* 3.2 15.8 + - - -
45D GLU* 3.1 21.8 + - - +
47D VAL* 5.0 7.6 - - + +
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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