Contacts of the strand formed by residues 40 - 45 (chain C) in PDB entry 2D1X
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 TRP 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C TYR* 3.4 21.1 - - - -
21C GLU* 4.1 11.4 - - + -
36C ILE* 3.1 22.8 + - + +
37C ASP* 3.0 27.1 + - - +
39C GLY* 1.3 77.4 - - - +
41C TRP* 1.3 75.4 + - - +
51C LEU* 4.2 13.7 - - + -
52C PHE* 3.3 43.7 - - - -
53C PRO* 3.6 15.5 - - + -
56D TYR* 3.8 11.4 - - - -
3Q LYS* 4.2 19.2 - - + +
4Q ARG* 2.7 48.2 + - + -
5Q PRO 4.1 0.9 - - - -
6Q PRO* 3.5 31.5 - - + -
7Q PRO* 4.4 0.4 - - + -
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Residues in contact with TRP 41 (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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33C ILE* 3.7 16.2 - - + -
34C GLU 3.3 10.3 - - - +
35C MET* 3.1 44.6 - - + +
36C ILE* 3.4 4.7 - - - -
37C ASP 3.6 11.7 + - - -
38C ASP* 4.5 2.2 + - - +
39C GLY 4.1 0.2 + - - -
40C TRP* 1.3 87.3 - - - +
42C ARG* 1.3 61.9 + - - +
51C LEU* 3.2 5.9 - - - +
52C PHE* 2.8 58.0 + + + -
54C ALA* 3.2 29.7 - - + +
57C VAL* 3.8 20.4 - - + -
59C LEU* 3.8 34.1 - - + -
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Residues in contact with ARG 42 (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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3A ASP 4.6 1.4 + - - -
32A ASN* 2.8 50.4 + - - +
44A VAL* 4.5 0.6 - - - +
49A TYR* 3.5 34.5 + - + -
32C ASN 3.7 1.2 - - - +
33C ILE* 3.3 2.1 - - - -
34C GLU* 2.9 69.0 + - + +
36C ILE* 3.6 22.3 - - + +
41C TRP* 1.3 74.4 - - - +
43C GLY* 1.3 58.7 + - - +
49C TYR* 3.8 11.5 + - + +
50C GLY* 3.0 17.3 - - - +
51C LEU* 3.4 12.6 - - + -
52C PHE* 3.5 4.3 - - - -
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Residues in contact with GLY 43 (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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22C ILE* 4.0 4.1 - - - +
30C ILE* 4.1 5.6 - - - -
31C THR 3.4 11.4 - - - -
32C ASN 3.7 7.6 - - - -
33C ILE* 4.3 0.4 - - - -
42C ARG* 1.3 75.8 - - - +
44C VAL* 1.3 65.1 + - - -
48C ARG 3.8 1.2 - - - +
49C TYR* 3.3 5.8 - - - -
50C GLY 3.0 29.5 + - - +
52C PHE* 3.3 11.8 - - - -
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Residues in contact with VAL 44 (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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42A ARG* 3.9 27.6 - - - +
29C ILE 3.8 0.9 - - - +
30C ILE* 3.2 5.3 - - - +
31C THR* 2.8 54.9 + - - +
32C ASN* 4.2 7.2 - - + +
43C GLY* 1.3 76.6 - - - -
45C CYS* 1.3 65.6 + - - +
46C LYS 4.9 0.2 - - - +
47C GLY* 4.2 22.4 - - - +
48C ARG 3.3 9.6 - - - +
49C TYR* 3.6 22.2 - - + -
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Residues in contact with CYS 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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22C ILE* 3.9 20.9 - - + -
23C SER 4.0 8.7 - - - +
24C PHE* 3.6 29.2 - - - -
28C ASP* 4.0 12.6 - - - -
29C ILE 3.5 18.6 - - - +
30C ILE* 4.2 8.5 - - + -
43C GLY 4.2 0.2 + - - -
44C VAL* 1.3 77.5 - - - +
46C LYS* 1.3 80.8 + - - +
47C GLY 3.2 0.4 - - - -
48C ARG* 2.9 26.2 + - - +
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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