Contacts of the strand formed by residues 40 - 44 (chain D) in PDB entry 2X6L
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 VAL 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D TYR* 3.9 10.1 - - + -
29D TYR 3.5 10.5 - - - +
30D GLU* 3.9 18.8 - - + +
39D ALA* 1.3 78.4 - - - +
41D VAL* 1.3 66.6 + - - +
42D PHE* 3.8 28.9 - - + -
51D CYS* 3.7 1.4 - - - -
52D ALA* 2.9 35.1 + - - +
54D PRO* 4.1 11.9 - - + -
59D VAL* 3.7 25.8 - - + -
63D VAL* 3.9 15.3 - - + -
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Residues in contact with VAL 41 (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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8B PRO* 4.3 9.0 - - + -
12D CYS* 4.0 14.6 - - - -
28D TYR* 3.1 5.0 - - - +
29D TYR* 2.8 84.8 + - + +
31D THR* 3.7 18.4 - - + -
40D VAL* 1.3 77.7 - - - +
42D PHE* 1.3 66.0 + - - +
49D GLN* 4.0 12.8 - - + +
50D VAL 3.6 22.4 - - - +
51D CYS* 4.6 0.2 - - - -
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Residues in contact with PHE 42 (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 LEU* 4.1 21.3 - - + -
25D VAL* 3.7 24.5 - - + -
27D ASP 3.6 0.9 - - - +
28D TYR* 3.8 15.7 - - + -
40D VAL* 3.8 21.1 - - + -
41D VAL* 1.3 75.4 - - - +
43D GLN* 1.3 60.6 + - - +
44D THR* 4.1 0.6 + - + -
48D LYS 3.6 0.9 - - - +
49D GLN* 3.4 5.6 - - - -
50D VAL* 3.0 34.9 + - - +
52D ALA* 3.5 32.1 - - + -
58D TRP* 3.8 21.1 - + - -
59D VAL* 3.9 27.1 - - + -
62D TYR* 3.9 21.8 - + + -
63D VAL* 4.3 4.3 - - + -
66D LEU* 4.4 3.1 - - + -
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Residues in contact with GLN 43 (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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25D VAL* 3.5 4.9 - - - -
26D VAL* 2.9 44.5 + - + +
27D ASP* 2.9 30.5 + - + +
28D TYR* 5.5 0.4 - - - -
29D TYR* 6.5 0.4 - - + -
41D VAL 4.0 0.8 + - - -
42D PHE* 1.3 73.0 - - - +
44D THR* 1.3 70.5 + - - +
47D SER* 4.0 20.8 + - - -
48D LYS 3.4 9.9 - - - +
49D GLN* 3.8 20.1 - - - +
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Residues in contact with THR 44 (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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67C GLU* 3.2 21.5 + - - +
18D ARG* 6.0 0.4 - - - +
20D LEU* 4.9 17.3 - - + -
24D PHE* 3.0 16.6 - - + +
25D VAL* 5.4 0.4 - - + -
26D VAL* 3.6 8.6 - - - +
42D PHE 4.7 0.2 - - - +
43D GLN* 1.3 87.3 + - - +
45D LYS* 1.3 59.2 + - - +
46D ARG* 3.4 3.8 + - - +
47D SER* 3.0 13.7 + - - -
48D LYS* 3.1 36.8 + - + +
50D VAL* 4.1 21.8 - - + -
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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