Contacts of the strand formed by residues 52 - 60 (chain C) in PDB entry 3A98
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 HIS 52 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C LEU* 2.8 22.8 + - + +
51C LYS* 1.3 108.2 + - + +
53C LYS* 1.3 59.9 + - - +
54C MSE 3.2 3.4 - - + -
55C LEU* 3.0 52.4 + - + +
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Residues in contact with LYS 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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48C TYR* 3.6 41.8 + - + +
49C LEU 3.4 4.9 - - - -
50C ILE* 3.2 39.0 + - - +
51C LYS 5.3 0.2 - - - -
52C HIS* 1.3 70.7 - - - +
54C MSE 1.3 75.2 + - + +
55C LEU 3.1 1.1 + - - -
56C GLN* 4.4 0.2 - - - +
727D ASN* 2.9 28.5 + - - +
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Residues in contact with MSE 54 (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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52C HIS 3.2 2.0 + - - -
53C LYS* 1.3 91.2 - - + +
55C LEU* 1.3 66.6 + - + +
56C GLN* 3.4 8.7 + - - +
727D ASN* 3.6 46.0 - - + +
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Residues in contact with LEU 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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27C LEU* 3.8 17.4 - - + +
48C TYR* 3.2 18.1 - - - +
49C LEU* 3.2 30.5 + - + -
52C HIS* 3.0 35.6 + - + +
54C MSE 1.3 83.8 - - + +
56C GLN* 1.3 58.9 + - - +
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Residues in contact with GLN 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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25C PRO* 4.6 2.1 - - - +
27C LEU* 4.2 10.5 - - - +
38C GLN* 2.9 33.0 + - - +
46C ARG* 3.6 30.9 + - + +
47C GLY 3.2 14.4 - - - +
48C TYR* 3.7 7.9 - - + -
54C MSE 3.4 8.0 + - - +
55C LEU* 1.3 74.6 - - - +
57C GLY* 1.3 61.1 + - - +
725D ASP 4.0 4.9 + - - -
726D CYS* 3.1 12.2 - - - +
727D ASN* 2.8 42.3 + - - +
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Residues in contact with GLY 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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25C PRO 3.2 13.2 - - - -
26C GLN 4.7 0.2 - - - -
27C LEU* 3.7 12.4 - - - +
46C ARG* 3.3 8.0 - - - -
47C GLY 2.8 31.8 + - - +
56C GLN* 1.3 80.2 - - - +
58C ILE* 1.3 66.6 + - - -
59C PHE* 3.5 5.0 - - - -
722D PHE* 6.3 0.4 - - - -
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Residues in contact with ILE 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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4C TRP* 3.7 25.4 - - + -
19C PHE* 3.9 3.5 - - - -
25C PRO* 2.9 18.5 + - + +
26C GLN* 3.4 22.7 - - + +
27C LEU 2.8 21.5 + - - +
44C TRP* 3.8 19.3 - - + -
45C TYR 3.2 9.9 - - - +
46C ARG* 3.9 5.6 - - + -
57C GLY* 1.3 77.1 - - - -
59C PHE* 1.3 64.1 + - - +
717D PRO* 3.9 26.2 - - + -
720D TYR* 4.0 15.9 - - + -
722D PHE* 3.8 22.2 - - + -
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Residues in contact with PHE 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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19C PHE* 3.9 7.4 - - + -
27C LEU* 4.0 16.6 - - + +
29C LEU* 3.6 21.1 - - + -
35C VAL* 4.1 25.8 - - + -
37C ILE* 4.5 3.8 - - + -
44C TRP* 3.3 8.2 - - - -
45C TYR* 2.9 48.2 + + + +
46C ARG 4.3 0.4 - - - -
47C GLY* 3.6 27.8 - - - -
57C GLY 3.5 17.0 - - - -
58C ILE* 1.3 79.3 - - - +
60C PRO* 1.3 73.1 - - + +
64C ILE* 3.7 37.7 - - + -
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Residues in contact with PRO 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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19C PHE* 3.7 29.6 - - + -
43C ASP 3.6 7.6 - - - +
44C TRP* 3.6 20.0 - - + -
45C TYR* 4.5 0.4 - - - -
59C PHE* 1.3 91.2 - - + +
61C LYS* 1.3 65.8 + - - +
62C SER* 3.8 3.8 - - - +
63C PHE* 3.2 34.1 + - + +
64C ILE* 3.6 12.3 - - - +
713D ILE* 4.8 0.4 - - + -
714D PRO* 3.7 29.4 - - + -
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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