Contacts of the strand formed by residues 42 - 49 (chain C) in PDB entry 2X1L
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 ASP 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C SER* 4.0 21.6 + - - +
3C GLU 2.9 13.5 + - - +
4C PRO* 3.2 6.2 - - + +
5C PHE 2.8 27.6 + - - -
40C GLY 4.1 0.8 + - - -
41C TYR* 1.3 68.5 - - - +
43C VAL* 1.3 58.1 + - - +
253C ARG* 3.3 27.1 + - - -
254C TYR* 2.7 32.6 + - - -
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Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 3.2 16.6 - - + +
7C ILE* 4.6 0.9 - - + -
33C ALA* 3.9 19.5 - - + +
36C LYS* 3.6 30.5 - - + -
37C ARG* 3.7 46.7 + - + +
41C TYR* 3.5 10.3 + - + +
42C ASP* 1.3 79.4 + - - +
44C ARG* 1.3 72.3 + - - +
45C TYR 4.3 0.2 - - - +
90C ASP* 3.5 12.5 - - - +
254C TYR* 4.3 4.1 + - - -
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Residues in contact with ARG 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE 2.9 7.8 + - - +
6C TYR* 3.3 21.8 - - + -
7C ILE* 3.0 28.4 + - - +
42C ASP 4.0 1.0 + - - -
43C VAL* 1.3 75.0 + - - +
45C TYR* 1.3 63.7 + - - +
46C LEU* 5.6 1.6 - - + -
90C ASP* 3.4 16.8 - - + +
240C GLY 3.6 26.5 + - - +
241C VAL* 3.7 13.8 - - - +
250C SER* 3.3 32.3 + - - -
253C ARG* 5.5 1.6 - - - +
254C TYR* 3.4 36.2 + - + -
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Residues in contact with TYR 45 (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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7C ILE* 3.5 14.1 - - + -
9C THR* 3.9 14.8 - - + +
26C TYR* 3.1 25.8 + - - +
29C THR* 3.5 25.1 - - + -
30C ASP* 3.2 31.3 + - - -
33C ALA* 3.5 19.5 - - + -
37C ARG* 3.9 8.3 - - - +
43C VAL* 4.5 0.2 - - + -
44C ARG* 1.3 75.0 - - - +
46C LEU* 1.3 71.3 + - - +
47C THR* 4.4 5.8 - - - -
82C GLN* 4.8 0.5 + - - -
87C ILE* 3.3 20.9 - - + +
88C SER* 3.6 18.4 - - - -
89C PHE* 3.7 8.0 - - + +
90C ASP* 2.7 41.8 + - - +
91C ARG 3.6 6.8 + - - -
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Residues in contact with LEU 46 (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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6C TYR* 3.2 34.1 - - + +
7C ILE 3.0 7.3 + - - -
8C THR* 3.3 9.2 - - + -
9C THR 3.1 24.7 + - - -
44C ARG* 4.1 2.6 - - + -
45C TYR* 1.3 78.5 - - - +
47C THR* 1.3 62.4 - - - +
91C ARG* 3.7 28.7 - - + +
93C ILE* 3.9 22.4 - - + -
236C ASN* 3.3 39.3 - - - +
237C TYR* 4.0 4.3 - - + -
240C GLY* 3.8 20.6 - - - +
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Residues in contact with THR 47 (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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9C THR* 2.6 32.8 + - - +
11C ILE* 4.1 4.3 - - - -
26C TYR* 3.9 2.8 - - - -
45C TYR* 4.2 4.7 + - + -
46C LEU* 1.3 76.0 - - - +
48C GLY* 1.3 62.7 + - - +
82C GLN* 3.0 38.3 + - - +
89C PHE* 3.7 28.9 - - + -
91C ARG 3.3 6.4 + - - +
92C PHE* 3.4 7.7 - - + -
93C ILE* 2.8 31.4 + - - +
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Residues in contact with GLY 48 (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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9C THR* 4.4 0.4 + - - -
10C ALA 4.5 0.7 - - - +
11C ILE* 3.5 12.9 - - - +
12C ALA* 3.3 15.9 + - - -
26C TYR* 4.4 8.3 + - - -
47C THR* 1.3 83.7 + - - +
49C THR* 1.3 67.6 + - - +
82C GLN* 5.0 0.2 + - - -
92C PHE* 3.7 21.6 - - - -
93C ILE 3.1 10.3 - - - -
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Residues in contact with THR 49 (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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11C ILE* 3.7 7.9 - - - +
12C ALA 3.4 11.9 - - - +
14C PRO* 4.3 9.0 - - + -
48C GLY* 1.3 80.0 - - - +
50C ASP* 1.3 59.6 + - - +
51C VAL* 3.8 2.9 - - - +
75C SER* 2.9 31.1 + - - +
78C PHE* 3.9 23.6 - - + -
92C PHE* 3.8 16.3 - - + -
93C ILE 2.9 7.8 + - - +
94C ARG* 3.3 18.4 - - - +
95C THR* 3.4 25.5 + - - +
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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