Contacts of the strand formed by residues 46 - 50 (chain D) in PDB entry 1L9X
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 46 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C TRP* 3.5 55.3 + - + +
288C GLN* 5.8 0.2 - - - +
9D LYS* 3.0 45.0 + - - +
10D PRO 2.9 9.9 + - - +
11D ILE* 3.3 25.3 - - + +
12D ILE* 2.8 25.1 + - - +
41D GLU* 5.0 1.8 - - - -
45D ALA* 1.3 76.5 - - - +
47D VAL* 1.3 65.1 + - - +
268D GLU* 2.9 30.7 + - - -
272D LEU* 4.1 26.7 - - + +
274D TYR* 3.6 14.1 - - + +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ILE 3.3 6.5 - - - +
14D ILE* 3.5 28.3 - - + -
32D ILE* 6.2 0.2 - - + -
37D VAL* 4.0 25.4 - - + +
40D LEU* 3.9 31.4 - - + -
41D GLU* 4.1 10.0 + - + -
45D ALA 4.8 0.2 - - - +
46D ARG* 1.3 81.7 - - - +
48D VAL* 1.3 71.6 + - - +
49D PRO* 4.6 1.1 - - + -
272D LEU* 3.4 8.1 - - - +
273D ILE* 2.8 48.6 + - + +
274D TYR* 5.9 0.2 - - - -
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ILE* 3.3 26.9 - - + -
12D ILE 3.0 10.5 + - - +
13D GLY* 3.1 7.7 - - - -
14D ILE 3.0 22.3 + - - -
47D VAL* 1.3 76.5 - - - +
49D PRO* 1.3 79.2 - - - +
50D VAL* 3.4 7.6 + - + -
62D LEU* 4.8 11.7 - - + -
66D ILE* 4.4 10.8 - - + -
262D PHE* 4.2 12.8 - - + -
271D ALA* 3.6 27.1 - - + +
272D LEU* 3.7 10.5 - - + -
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Residues in contact with PRO 49 (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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14D ILE* 3.7 7.0 - - + +
16D MET* 4.1 7.8 - - + +
32D ILE* 3.6 22.7 - - + -
47D VAL* 4.1 0.9 - - + +
48D VAL* 1.3 90.9 - - - +
50D VAL* 1.3 60.4 + - - +
51D ARG* 3.9 3.3 + - - +
62D LEU* 5.7 0.9 - - - +
271D ALA 3.3 15.0 - - - +
273D ILE* 3.9 23.8 - - + +
276D PHE* 3.8 25.6 - - + -
293D PHE* 3.7 20.0 - - + -
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Residues in contact with VAL 50 (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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13D GLY* 3.9 4.3 - - - -
14D ILE 2.8 15.6 + - - +
15D LEU* 3.7 21.9 - - + -
16D MET* 3.0 30.6 + - - +
48D VAL* 3.6 19.1 - - + +
49D PRO* 1.3 72.0 - - - +
51D ARG* 1.3 74.1 + - - +
52D LEU* 4.3 0.7 - - - +
59D TYR* 4.0 7.4 - - + -
62D LEU* 4.3 11.9 - - + -
66D ILE* 5.0 3.4 - - + -
69D ILE* 3.7 24.2 - - + -
90D PHE* 4.0 22.9 - - + -
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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
------------------------------------------------------------
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