Contacts of the strand formed by residues 49 - 56 (chain S) in PDB entry 1YIT
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 VAL 49 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38S ALA* 3.6 20.0 - - + +
41S VAL* 4.1 13.2 - - + -
42S GLU* 2.6 40.7 + - + +
47S VAL* 4.7 0.7 - - + -
48S THR* 1.3 75.0 - - - +
50S GLU* 1.3 68.5 + - - +
51S GLN* 4.0 5.6 - - - +
52S VAL* 3.5 31.9 - - + -
66S VAL* 3.5 23.1 - - + -
67S ARG 3.8 2.9 - - - -
68S LEU* 4.4 4.7 - - + +
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Residues in contact with GLU 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48S THR* 3.6 13.0 + - - +
49S VAL* 1.3 77.4 - - - +
51S GLN* 1.3 60.6 + - - +
67S ARG* 2.8 41.2 + - - +
68S LEU 3.9 2.9 - - - +
69S SER* 3.3 42.2 - - - +
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Residues in contact with GLN 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15070 C 3.7 18.2 + - - -
15080 C 4.3 13.0 + - - -
23S LYS* 6.0 1.0 - - - +
49S VAL* 4.6 0.2 - - - -
50S GLU* 1.3 81.6 - - - +
52S VAL* 1.3 72.3 + - - +
53S ASN* 3.2 26.3 + - - +
65S VAL 4.0 0.7 - - - +
66S VAL* 3.6 0.2 - - - -
67S ARG* 3.0 62.0 + - - +
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Residues in contact with VAL 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34S LYS* 3.2 51.1 + - + +
37S VAL* 3.9 27.8 - - + -
38S ALA* 4.0 9.2 - - + -
49S VAL* 3.5 22.9 - - + -
51S GLN* 1.3 84.1 - - - +
53S ASN* 1.3 73.0 + - - +
54S THR* 4.2 6.1 - - + -
64S ALA* 4.3 0.9 - - + -
65S VAL 3.6 2.5 - - - -
66S VAL* 4.0 16.8 - - + -
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Residues in contact with ASN 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14470 U 3.3 42.1 + - - +
14480 A 3.8 10.0 - - - +
15070 C 2.9 30.9 + - - +
34S LYS* 5.4 1.0 - - - +
51S GLN* 3.2 30.3 - - - +
52S VAL* 1.3 81.7 + - - +
54S THR* 1.3 61.3 + - - +
63S LYS 3.9 0.2 - - - +
64S ALA* 3.3 2.9 - - - +
65S VAL* 2.7 45.1 + - + +
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Residues in contact with THR 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14470 U 3.4 19.2 - - - +
14480 A 3.5 12.4 + - - -
16740 C 4.3 4.4 + - - +
16750 C 4.2 14.4 + - - -
80280 MG 4.2 2.4 - - - -
34S LYS* 3.8 36.4 - - + +
37S VAL* 4.7 3.8 - - + -
52S VAL* 4.2 5.2 - - + -
53S ASN* 1.3 80.3 - - - +
55S GLN* 1.3 64.8 + - - +
62S LYS* 4.0 23.0 - - + +
63S LYS 3.2 6.3 - - - -
64S ALA* 4.2 13.9 - - + -
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Residues in contact with GLN 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14460 U 3.0 77.5 + - - +
14470 U 4.3 13.6 - - - +
16770 U 6.3 1.6 - - + -
82 LYS* 5.7 1.0 - - - +
54S THR* 1.3 78.9 - - - +
56S ASN* 1.3 68.7 + - - +
57S THR* 3.4 23.6 + - - +
58S MET 5.5 0.2 - - - +
62S LYS* 3.2 4.3 - - - +
63S LYS* 2.7 54.5 + - + +
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Residues in contact with ASN 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16750 C 2.9 35.1 + - - -
16760 G 2.9 39.4 + - - +
16770 U 4.5 0.3 + - - -
52 LYS* 3.8 18.4 - - + +
82 LYS* 2.9 31.1 + - + -
30S ASP* 3.8 4.5 - - - +
55S GLN* 1.3 73.9 - - - +
57S THR* 1.3 61.5 + - - +
61S GLU 4.0 3.1 - - - +
62S LYS* 3.5 26.9 + - - +
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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