Contacts of the helix formed by residues 33 - 46 (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 SER 33 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16730 U 3.5 24.5 + - - -
16740 C 3.2 13.7 - - - -
31S ARG 3.9 1.4 + - - -
32S ALA* 1.3 74.1 - - - +
34S LYS* 1.3 65.3 + - - +
35S GLY* 3.5 5.0 + - - -
36S GLU* 2.7 38.0 + - - +
37S VAL* 2.9 25.9 + - - +
54S THR* 5.3 0.2 - - - -
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Residues in contact with LYS 34 (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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14480 A 2.8 39.0 + - - +
14490 G 4.8 4.9 + - - -
16730 U 4.0 31.6 + - - +
16740 C 2.9 36.0 + - - +
33S SER* 1.3 72.5 - - - +
35S GLY* 1.3 58.6 + - - +
37S VAL* 3.2 5.9 + - - +
38S ALA* 2.8 29.7 + - - +
52S VAL* 3.2 40.6 + - + +
53S ASN* 5.4 1.0 - - - +
54S THR* 3.8 22.8 - - + +
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Residues in contact with GLY 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16720 G 5.9 3.1 - - - -
16730 U 5.0 3.8 + - - -
33S SER* 3.2 6.7 + - - -
34S LYS* 1.3 79.4 - - - +
36S GLU* 1.3 57.3 + - - +
38S ALA* 3.4 7.1 - - - +
39S ASP* 3.1 35.6 + - - +
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Residues in contact with GLU 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2S TRP* 4.2 9.3 - - - -
4S VAL* 4.4 13.1 - - + +
31S ARG 3.6 5.4 - - - +
32S ALA* 3.0 17.3 - - + +
33S SER* 2.7 40.2 + - - +
35S GLY* 1.3 71.4 - - - +
37S VAL* 1.3 68.5 + - - +
38S ALA 3.0 1.9 + - - -
39S ASP* 3.1 8.1 + - - +
40S ALA* 2.9 26.9 + - - +
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Residues in contact with VAL 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S VAL* 4.1 9.2 - - - +
5S ILE* 5.8 0.4 - - + -
26S PHE* 5.6 0.9 - - + -
28S VAL* 4.1 32.8 - - + -
32S ALA* 4.2 10.1 - - + +
33S SER 2.9 23.7 + - - +
34S LYS* 3.4 9.0 - - - +
36S GLU* 1.3 75.9 - - - +
38S ALA* 1.3 60.9 + - - +
40S ALA* 3.9 0.3 - - - +
41S VAL* 2.9 37.7 + - + +
52S VAL* 3.9 12.6 - - + -
54S THR* 4.7 3.8 - - + -
64S ALA* 3.7 26.9 - - + -
66S VAL* 4.0 10.8 - - + -
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Residues in contact with ALA 38 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34S LYS 2.8 13.6 + - - +
35S GLY* 3.4 13.2 - - - +
36S GLU 3.0 0.2 - - - -
37S VAL* 1.3 73.9 - - - +
39S ASP* 1.3 72.4 + - - +
41S VAL* 3.1 4.9 + - - +
42S GLU* 2.9 27.5 + - + +
49S VAL* 3.6 24.6 - - + +
52S VAL* 4.0 10.7 - - + +
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Residues in contact with ASP 39 (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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35S GLY 3.1 17.4 + - - +
36S GLU* 3.7 7.5 - - - +
38S ALA* 1.3 80.0 - - - +
40S ALA* 1.3 66.4 + - - +
42S GLU* 2.8 27.5 + - - +
43S GLU* 2.9 32.9 + - - +
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Residues in contact with ALA 40 (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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4S VAL* 3.7 32.5 - - + -
5S ILE* 3.8 14.1 - - + -
36S GLU 2.9 19.3 + - - +
37S VAL 3.9 1.3 - - - +
39S ASP* 1.3 71.7 - - - +
41S VAL* 1.3 58.0 + - - +
43S GLU* 3.3 10.6 + - - +
44S GLN* 2.9 34.7 + - + +
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Residues in contact with VAL 41 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5S ILE* 3.8 19.7 - - + -
24S LEU* 5.4 2.0 - - + -
26S PHE* 4.1 27.6 - - + -
37S VAL* 2.9 32.7 + - + +
38S ALA 3.1 4.2 + - - +
39S ASP 3.1 0.8 - - - -
40S ALA* 1.3 74.7 - - - +
42S GLU* 1.3 66.5 + - - +
45S TYR* 3.0 36.2 + - + +
47S VAL* 4.2 11.2 - - + +
49S VAL* 4.1 15.9 - - + -
66S VAL* 4.4 9.4 - - + -
68S LEU* 4.7 4.7 - - + -
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Residues in contact with GLU 42 (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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38S ALA* 2.9 21.4 + - - +
39S ASP* 2.8 21.6 + - - +
41S VAL* 1.3 72.7 - - - +
43S GLU* 1.3 60.2 + - + +
46S ASP* 2.9 27.2 + - - -
47S VAL* 3.4 21.3 + - - +
48S THR* 3.4 10.2 - - - +
49S VAL* 2.6 43.8 + - + +
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Residues in contact with GLU 43 (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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39S ASP* 2.9 42.4 + - - +
40S ALA* 3.6 8.0 + - - +
42S GLU* 1.3 81.0 - - + +
44S GLN* 1.3 66.7 + - + +
45S TYR 3.7 0.2 + - - -
46S ASP* 4.2 4.3 + - - +
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Residues in contact with GLN 44 (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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5S ILE* 4.4 10.1 - - + -
40S ALA* 2.9 19.0 + - + +
43S GLU* 1.3 80.9 - - + +
45S TYR* 1.3 83.2 + - + +
24V LYS* 5.8 1.6 + - - +
25V THR* 4.3 21.4 + - - +
28V LEU* 3.3 29.9 - - + +
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Residues in contact with TYR 45 (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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5S ILE* 4.2 12.6 - - + +
8S PRO* 4.4 5.0 - - - +
24S LEU* 5.5 0.7 - - + -
26S PHE* 3.5 33.9 - + - -
41S VAL* 3.0 22.6 + - + +
44S GLN* 1.3 99.6 - - + +
46S ASP* 1.3 76.0 + - - +
47S VAL* 3.7 9.7 - - + +
77S VAL* 3.5 33.9 - - + -
78S ALA* 6.1 0.2 - - - -
80S ARG* 2.8 29.9 + - + +
81S ILE* 3.7 36.6 - - + +
28V LEU* 4.6 14.8 - - + +
29V ASN* 5.8 0.8 + - - -
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Residues in contact with ASP 46 (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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42S GLU 2.9 18.7 + - - -
43S GLU 4.2 3.4 + - - +
44S GLN 3.7 1.0 - - - -
45S TYR* 1.3 86.3 - - - +
47S VAL* 1.3 63.0 + - - +
72S ASP* 4.7 1.7 - - - +
80S ARG* 4.4 2.5 + - - +
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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