Contacts of the strand formed by residues 56 - 62 (chain C) in PDB entry 5ITY
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 LEU 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C LEU* 3.8 18.2 - - + +
10C ALA* 3.8 17.3 - - + -
11C SER* 3.7 30.1 - - - +
14C VAL* 5.3 1.6 - - + -
49C ALA* 5.0 3.8 - - + -
50C SER 3.8 10.3 - - - +
51C ALA* 4.4 0.7 - - + +
55C GLU* 1.3 75.5 - - - +
57C ARG* 1.3 72.4 + - - +
58C LEU* 4.1 7.6 - - + +
76C VAL* 3.3 4.3 - - - +
77C PHE* 2.7 63.4 + - + +
79C PHE* 4.4 5.4 - - + -
85C PHE* 4.0 20.9 - - + -
129C TRP* 3.9 3.1 - - - -
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Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 3.1 6.6 - - - -
50C SER* 2.8 53.8 + - - +
56C LEU* 1.3 77.4 - - - +
58C LEU* 1.3 67.9 + - - +
59C ILE* 4.0 6.5 + - + +
74C ALA* 4.4 14.8 - - + -
75C LEU 3.0 11.4 - - - +
76C VAL* 5.1 2.2 - - + +
127C GLY* 3.9 30.1 + - - -
128C LYS* 4.1 8.5 - - - +
129C TRP* 3.3 56.2 - - + +
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Residues in contact with LEU 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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14C VAL* 4.1 10.8 - - + -
47C ILE* 3.4 28.0 - - + -
48C SER 3.2 15.7 - - - +
49C ALA* 5.0 1.6 - - + -
56C LEU* 4.1 8.1 - - + +
57C ARG* 1.3 73.8 - - - +
59C ILE* 1.3 62.4 + - - +
60C LEU* 4.0 8.5 + - + +
74C ALA* 3.0 6.4 - - - +
75C LEU* 2.6 48.4 + - + -
77C PHE* 3.5 16.8 - - + -
85C PHE* 3.4 34.8 - - + -
101C PHE* 4.1 20.4 - - + -
112C LEU* 4.9 3.1 - - + -
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Residues in contact with ILE 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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46C ARG 3.9 0.3 - - - +
47C ILE* 3.4 8.5 - - - +
48C SER* 2.7 64.1 + - - +
49C ALA 4.9 2.9 - - - +
50C SER* 4.8 13.2 - - - +
57C ARG* 4.9 5.8 - - + +
58C LEU* 1.3 73.1 - - - +
60C LEU* 1.3 63.3 + - - +
61C SER* 2.9 27.8 - - - +
72C PRO* 5.7 1.6 - - + -
73C LEU 5.2 1.1 - - - +
74C ALA* 3.9 15.5 - - + -
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Residues in contact with LEU 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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27C VAL* 4.0 4.3 - - + -
38C VAL* 5.4 2.5 - - + -
40C PHE* 3.6 39.6 - - + -
45C TYR* 3.7 15.7 - - + -
46C ARG 3.9 2.9 - - - -
47C ILE* 3.9 12.6 - - + -
58C LEU* 4.4 22.9 - - + +
59C ILE* 1.3 76.5 - - - +
61C SER* 1.3 62.8 + - - +
62C PRO* 3.9 3.4 - - - +
72C PRO* 3.5 1.9 - - - +
73C LEU 3.1 40.9 + - - +
75C LEU* 4.6 10.1 - - + -
101C PHE* 3.7 33.9 - - + -
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Residues in contact with SER 61 (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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45C TYR* 3.3 5.4 - - - +
46C ARG* 3.0 39.6 + - - +
59C ILE* 2.9 28.1 - - - +
60C LEU* 1.3 72.6 + - - +
62C PRO* 1.4 70.4 - - - +
63C LEU* 4.6 1.4 - - - +
72C PRO* 3.8 14.7 - - - +
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Residues in contact with PRO 62 (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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40C PHE* 4.0 7.6 - - + -
42C SER* 3.3 30.3 - - - +
44C ALA 3.9 4.0 - - - +
45C TYR* 3.9 1.3 - - + -
60C LEU 3.9 1.6 - - - +
61C SER* 1.4 90.9 - - - +
63C LEU* 1.3 61.5 + - - +
64C PRO* 4.9 0.2 - - - +
66C ALA* 4.5 5.4 - - + -
68C PRO 5.6 1.6 - - - +
70C GLN* 3.6 32.1 - - + +
72C PRO* 3.8 27.7 - - + +
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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