Contacts of the strand formed by residues 49 - 54 (chain H) in PDB entry 1C9T
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 GLU 49 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H ALA* 3.6 11.8 - - - +
28H CYS* 5.1 1.4 - - - +
29H SER 4.8 8.9 + - - +
31H LEU 5.5 0.3 - - - +
32H HIS* 3.8 26.6 + - + +
41H PHE* 3.6 24.5 + - + +
42H LYS 3.1 10.3 - - - +
43H LYS* 3.1 42.1 + - + -
47H GLY 4.4 0.9 - - - +
48H CYS* 1.3 76.3 - - - +
50H TYR* 1.3 63.7 + - - +
51H ALA 3.5 1.7 + - - -
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Residues in contact with TYR 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLY* 3.9 15.0 - - - -
18H ALA* 3.7 25.1 - - + -
32H HIS* 3.3 10.3 + - - -
41H PHE* 3.3 11.3 - - - +
42H LYS* 2.6 49.1 + - + +
44H ASP* 3.6 38.2 - - + +
49H GLU* 1.3 71.2 - - - +
51H ALA* 1.3 68.1 + - - +
52H CYS 3.2 0.9 + - - +
53H ILE* 3.5 42.3 + - + +
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Residues in contact with ALA 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASN 6.0 2.2 - - - +
99B LEU* 5.8 3.4 - - + -
18H ALA* 5.2 0.2 - - - +
31H LEU* 3.4 41.7 - - + +
32H HIS* 2.7 33.2 - - - -
33H CYS 3.3 1.3 + - - +
41H PHE* 3.1 5.2 - - - -
49H GLU 3.5 3.6 + - - -
50H TYR* 1.3 70.2 - - - +
52H CYS* 1.3 61.8 + - + +
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Residues in contact with CYS 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B HIS* 3.6 27.4 - - - -
94B TYR* 5.4 0.9 - - - +
96B SER 5.3 5.2 - - - +
99B LEU* 4.8 13.2 - - + -
33H CYS* 2.0 50.0 - - + -
35H VAL* 4.2 3.1 - - - -
41H PHE* 3.9 2.5 - - - -
50H TYR* 3.3 1.0 - - - +
51H ALA* 1.3 79.4 - - + +
53H ILE* 1.3 66.5 + - - +
54H CYS* 5.7 1.3 - - - -
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Residues in contact with ILE 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H PHE* 3.3 11.9 - - - +
42H LYS* 2.8 50.7 + - + +
50H TYR* 3.5 44.7 + - + +
52H CYS* 1.3 83.6 - - - +
54H CYS* 1.3 65.8 + - - +
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Residues in contact with CYS 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 6.0 1.1 - - - -
60B LYS* 6.3 1.3 - - - -
35H VAL* 5.0 12.3 - - - -
36H LYS 4.9 0.7 - - - -
37H CYS* 2.0 56.1 - - + -
38H GLU 5.3 0.7 - - - +
40H GLY 3.5 3.6 - - - -
41H PHE* 4.9 1.3 - - - -
42H LYS* 3.6 18.7 + - - -
52H CYS 5.7 0.4 - - - -
53H ILE* 1.3 79.5 - - - +
55H ALA* 1.3 67.2 + - - +
56H ASP* 3.7 2.3 + - - +
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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