Contacts of the strand formed by residues 52 - 60 (chain C) in PDB entry 2X7N
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 MET 52 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 3.8 5.2 - - - +
35C LYS* 3.0 26.4 + - + -
36C GLY* 3.1 31.3 + - - +
50C GLY 3.8 0.6 + - - -
51C ASP* 1.3 75.0 - - - +
53C VAL* 1.3 61.4 + - - +
70C PRO* 3.2 34.1 - - + -
71C ALA 3.2 16.2 - - - +
72C ILE* 4.3 7.0 - - + +
98C ALA* 4.6 9.9 - - + -
99C ASN 4.2 16.4 - - - +
100C PRO* 6.2 0.4 - - + -
101C LYS 5.9 0.2 - - - +
102C GLY* 5.5 0.7 - - - -
121C TRP* 3.7 35.9 - - + +
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Residues in contact with VAL 53 (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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18C MET* 5.4 3.1 - - + -
31C ILE* 3.6 31.0 - - + -
33C ALA 2.7 25.1 - - - +
34C VAL* 4.3 10.3 - - + +
35C LYS* 4.3 3.4 - - - +
47C ALA* 5.2 1.1 - - + -
52C MET* 1.3 76.8 - - - +
54C MET* 1.3 74.2 + - - +
55C ALA* 5.1 1.3 - - + -
70C PRO* 3.4 4.0 - - - +
71C ALA* 2.8 52.8 + - + +
72C ILE 4.5 0.7 - - - +
73C VAL* 4.5 20.4 - - + -
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Residues in contact with MET 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ILE* 2.8 46.1 + - + +
33C ALA* 2.8 12.3 + - + +
35C LYS* 3.6 39.6 - - + +
53C VAL* 1.3 85.2 - - - +
55C ALA* 1.3 61.9 + - - +
68C VAL* 3.5 28.3 - - + -
69C MET 3.6 7.6 - - - +
70C PRO* 4.4 9.6 - - + -
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Residues in contact with ALA 55 (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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29C LEU* 4.1 30.5 - - + -
30C TYR 3.2 15.5 - - - +
31C ILE* 4.7 6.1 - - + -
32C ILE* 4.2 3.8 - - - -
53C VAL* 5.0 1.3 - - + -
54C MET* 1.3 75.8 - - - +
56C THR* 1.4 59.9 + - - +
57C VAL* 5.9 0.4 - - - -
67C LYS 3.8 0.2 - - - +
68C VAL* 3.2 9.0 - - - +
69C MET* 2.6 41.4 + - + +
71C ALA* 4.9 8.3 - - + -
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Residues in contact with THR 56 (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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29C LEU* 3.6 4.4 - - - +
30C TYR* 3.0 54.0 + - + +
32C ILE* 5.1 8.7 - - + +
55C ALA* 1.4 75.0 - - - +
57C VAL* 1.4 65.1 + - - +
58C LYS* 4.7 1.8 - - + +
66C LYS* 4.0 17.0 + - - +
67C LYS 3.4 9.8 + - - -
68C VAL* 4.4 10.3 - - - +
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Residues in contact with VAL 57 (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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26C ALA* 3.8 19.7 - - + -
28C ASN 3.9 3.8 - - - +
29C LEU* 3.8 15.5 - - + -
55C ALA 5.9 0.2 - - - -
56C THR* 1.4 75.6 + - - +
58C LYS* 1.4 60.4 + - - +
59C LYS 3.3 28.0 - - - +
64C LEU* 3.5 27.4 - - + +
65C ARG* 3.7 18.1 - - - +
66C LYS* 3.0 22.4 + - - +
67C LYS* 3.2 14.6 + - + +
69C MET* 5.8 4.9 - - + -
97C ILE* 5.0 6.5 - - + -
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Residues in contact with LYS 58 (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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17C ILE* 5.4 11.4 - - + +
28C ASN* 2.7 35.9 + - - +
29C LEU 5.0 1.3 - - - -
30C TYR* 4.9 18.8 - - + -
56C THR* 3.4 6.4 + - + -
57C VAL* 1.4 74.4 - - - +
59C LYS* 1.3 70.7 + - + +
65C ARG* 4.3 13.6 + - - +
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Residues in contact with LYS 59 (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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27C ARG* 2.8 60.0 + - + +
28C ASN* 2.6 44.0 + - - +
57C VAL* 3.3 12.8 - - - +
58C LYS* 1.3 89.2 - - + +
60C GLY* 1.3 62.3 + - - +
65C ARG* 5.0 6.7 - - - +
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Residues in contact with GLY 60 (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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25C GLY 3.3 14.1 - - - -
26C ALA* 4.2 1.6 - - - -
27C ARG* 3.8 14.4 + - - -
57C VAL* 4.5 2.4 - - - +
59C LYS* 1.3 83.7 - - - +
61C LYS* 1.4 67.9 + - - +
62C PRO* 3.9 0.9 - - - +
65C ARG* 3.2 23.0 + - - +
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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