Contacts of the strand formed by residues 11 - 15 (chain C) 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 ILE 11 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LYS 3.7 9.2 - - - +
10C PRO* 1.3 78.9 - - - +
12C ILE* 1.3 63.1 + - - +
46C ARG* 3.3 28.7 - - + +
48C VAL* 3.4 31.6 - - + -
65C SER 5.4 0.9 - - - +
66C ILE* 3.7 11.9 - - + +
67C ASN* 2.7 45.1 + - - +
261C HIS* 6.5 0.7 - - - -
262C PHE* 3.9 13.9 - - + -
268C GLU* 3.7 38.1 - - + +
272C LEU* 4.1 9.0 - - + -
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Residues in contact with ILE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PRO 5.0 0.2 - - - -
11C ILE* 1.3 81.2 - - - +
13C GLY* 1.3 74.9 + - - +
14C ILE* 4.6 0.2 - - - +
40C LEU* 3.7 19.3 - - + -
45C ALA* 4.1 12.6 - - + -
46C ARG 2.9 11.4 + - - +
47C VAL* 3.3 10.6 - - - +
48C VAL* 3.0 20.7 + - - -
68C GLY* 3.5 15.3 - - - +
69C ILE* 4.0 0.9 - - - +
70C LEU 4.3 0.7 - - - +
251C PHE* 3.7 36.1 - - + -
252C VAL* 4.0 26.2 - - + -
255C ALA* 4.1 25.6 - - + -
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Residues in contact with GLY 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 1.3 80.2 - - - +
14C ILE* 1.3 61.2 + - - +
48C VAL* 3.0 14.8 - - - -
50C VAL* 3.9 5.2 - - - -
66C ILE* 4.0 9.8 - - - +
68C GLY 3.0 11.5 + - - -
69C ILE* 3.4 16.9 - - - +
70C LEU 2.9 25.3 + - - -
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Residues in contact with ILE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLY* 1.3 78.8 - - - +
15C LEU* 1.3 73.5 + - - +
16C MET 3.6 0.2 + - - -
32C ILE* 3.6 25.3 - - + +
36C TYR* 3.9 27.6 - - + +
37C VAL* 4.0 10.3 - - + +
40C LEU* 3.8 25.1 - - + -
47C VAL* 3.6 24.7 - - + -
48C VAL 3.0 7.7 + - - +
50C VAL* 2.8 27.3 + - - +
69C ILE* 4.7 0.2 - - - -
70C LEU* 3.5 13.5 - - + +
72C PRO* 3.9 18.6 - - + -
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ILE* 1.3 76.9 - - - +
16C MET* 1.3 68.6 + - - +
17C GLN* 5.0 0.2 + - - -
31C TYR 4.6 0.7 - - - +
32C ILE* 3.8 4.8 - - - +
50C VAL* 3.8 18.4 - - + -
52C LEU* 4.5 3.4 - - + -
69C ILE* 4.5 9.9 - - + -
70C LEU 3.3 6.8 + - - +
71C PHE* 3.5 31.6 - - + -
72C PRO* 3.4 27.8 - - + +
83C TYR* 3.9 37.0 - - + +
86C VAL* 3.6 28.3 - - + -
87C ALA* 3.9 11.2 - - + -
90C PHE* 4.7 4.3 - - + -
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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