Contacts of the strand formed by residues 47 - 59 (chain E) in PDB entry 1YI5
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 47 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.4 29.6 - - + +
118A ARG* 5.9 0.9 + - - -
40E GLU 4.0 0.7 - - - +
41E VAL* 3.7 3.6 - - - +
42E ASN* 3.1 32.0 + - + +
45E THR* 3.1 33.0 + - - +
46E ASN* 1.3 74.6 - - - +
48E VAL* 1.3 64.4 + - - +
92E ILE* 3.8 22.1 - - + +
120E ARG* 2.7 45.6 + - - +
121E PHE 3.7 2.9 - - - -
122E SER* 5.9 0.2 - - - -
125E VAL* 3.8 0.8 - - - +
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Residues in contact with VAL 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ILE* 5.0 11.2 - - + -
40E GLU 3.5 5.2 - - - +
41E VAL* 4.7 6.1 - - + -
47E GLU* 1.3 79.6 - - - +
49E ASP* 1.3 74.9 - - - +
50E VAL* 4.0 15.5 - - + -
119E GLN 4.1 0.5 - - - +
120E ARG* 3.1 10.1 - - - +
121E PHE* 2.9 39.9 + - + +
123E CYS* 4.0 15.7 - - - -
125E VAL* 3.8 22.0 - - + -
136E CYS* 4.4 7.2 - - - -
138E ILE* 6.3 0.7 - - + -
199E LEU* 5.5 5.2 - - + -
201E PHE* 4.7 14.6 - - + -
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Residues in contact with ASP 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ILE* 3.8 0.9 - - - -
39E LEU* 2.8 31.9 + - + +
40E GLU* 2.9 40.1 + - + +
48E VAL* 1.3 76.5 - - - +
50E VAL* 1.3 62.1 + - - +
118E ARG* 3.5 43.0 + - - +
119E GLN 3.9 2.2 - - - +
120E ARG* 3.1 36.7 + - - +
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Residues in contact with VAL 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E PHE* 3.4 38.1 - - + -
37E ASN 3.6 9.9 - - - +
38E ILE* 4.5 10.5 - - + -
48E VAL* 4.0 11.7 - - + -
49E ASP* 1.3 75.9 + - - +
51E VAL* 1.3 83.0 + - - +
52E PHE* 4.0 7.9 - - + -
117E ILE 3.9 0.2 - - - +
118E ARG* 3.5 2.6 - - - +
119E GLN 3.1 37.0 + - - +
121E PHE* 3.4 28.9 - - + -
138E ILE* 4.9 0.9 - - + -
199E LEU* 5.5 1.1 - - + -
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Residues in contact with VAL 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ALA 4.8 5.6 - - - +
92D ILE* 4.9 8.1 - - + +
36E ILE* 2.9 39.0 + - + +
37E ASN* 2.9 23.8 + - + +
39E LEU* 4.1 17.5 - - + -
50E VAL* 1.3 86.0 - - - +
52E PHE* 1.3 65.6 + - - +
98E LEU* 4.6 9.0 - - + -
116E SER* 4.3 13.9 - - - +
117E ILE 3.0 15.5 - - - +
118E ARG* 4.1 18.6 - - + -
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Residues in contact with PHE 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 3.7 41.7 - - + -
34E LYS 3.4 16.6 - - - +
35E PHE* 4.1 16.6 - + + -
36E ILE* 3.7 3.1 - - - -
50E VAL* 4.0 15.5 - - + -
51E VAL* 1.3 78.5 - - - +
53E TRP* 1.3 68.1 + - - +
54E GLN* 3.8 10.1 - - + -
117E ILE* 2.8 74.3 + - + +
119E GLN* 4.2 11.4 - - + -
121E PHE* 3.7 26.9 - + - -
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Residues in contact with TRP 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D TYR* 4.7 28.5 + + - -
143D TRP* 3.6 28.9 - + - -
32E SER 3.4 0.2 - - - +
34E LYS* 3.0 34.9 + - + +
36E ILE* 3.3 36.3 - - + +
51E VAL* 5.6 0.2 - - - +
52E PHE* 1.3 77.4 - - - +
54E GLN* 1.3 52.1 + - - +
55E GLN* 2.7 18.1 + - - +
114E MET* 3.7 30.7 - - + -
115E PRO 3.2 8.1 - - - +
116E SER* 3.5 30.4 + - - -
164E TYR* 5.0 19.5 - + - -
28I ALA* 4.8 18.4 - - + -
29I PHE* 4.0 25.6 - + + -
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Residues in contact with GLN 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E VAL* 4.7 10.8 - - + -
32E SER 3.3 5.4 - - - -
33E LEU* 3.7 19.4 - - + +
52E PHE* 3.7 11.9 + - + -
53E TRP* 1.3 65.2 - - - +
55E GLN* 1.3 52.5 + - - +
56E THR* 2.4 47.8 + - - +
86E LEU* 4.3 18.5 - - - +
87E ALA* 6.0 0.2 - - - -
113E TYR* 6.3 0.6 - - - -
114E MET* 4.4 0.2 - - - -
115E PRO* 3.1 25.7 + - + +
117E ILE* 3.5 27.7 - - + +
119E GLN* 5.5 1.9 - - - +
140E ILE* 3.8 21.5 - - + +
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Residues in contact with GLN 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E SER 3.6 1.9 - - - +
31E VAL* 3.4 4.6 - - - -
32E SER* 2.7 49.8 + - - +
34E LYS* 3.7 15.2 - - + +
53E TRP 2.7 13.0 + - - +
54E GLN* 1.3 66.4 - - - +
56E THR* 1.3 59.1 + - - +
57E THR* 4.9 2.7 - - - +
114E MET* 3.7 20.4 - - + +
28I ALA 3.5 19.1 - - - +
31I SER* 2.9 37.0 - - - +
32I ILE* 3.2 41.8 - - + +
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Residues in contact with THR 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E VAL* 4.5 7.4 - - + -
30E SER 3.7 2.0 - - - +
31E VAL* 4.6 3.1 - - + +
54E GLN* 2.4 41.3 + - - +
55E GLN* 1.3 73.5 - - - +
57E THR* 1.3 73.0 + - - +
58E TRP* 3.6 22.0 - - + -
84E PRO* 4.1 7.0 - - + -
86E LEU* 3.9 26.9 - - + -
112E LEU* 3.8 1.9 - - - -
113E TYR* 2.8 39.1 + - + +
114E MET* 4.9 1.2 - - - +
115E PRO* 4.3 2.4 - - - +
32I ILE* 5.6 0.9 - - - +
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Residues in contact with THR 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E VAL* 3.4 3.6 - - - +
30E SER* 2.9 51.7 + - - +
55E GLN* 4.8 2.8 - - - +
56E THR* 1.3 87.2 + - - +
58E TRP* 1.3 75.1 + - - +
110E GLU* 4.5 13.5 - - + +
111E VAL 3.2 12.6 - - - +
112E LEU* 3.8 21.0 - - + +
32I ILE* 4.5 10.7 - - - +
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Residues in contact with TRP 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E PRO* 5.7 0.4 - - + -
27E VAL* 4.4 10.5 - - + -
28E ALA 3.4 14.8 - - - +
29E VAL* 4.5 5.6 - - + -
56E THR* 3.6 31.0 - - + -
57E THR* 1.3 105.7 - - - +
59E SER* 1.3 63.8 + - - +
60E ASP* 4.2 13.4 + - + +
78E ILE* 5.7 1.8 - - + -
81E LEU* 5.8 1.3 - - + -
82E TRP* 3.4 44.9 + + - -
83E VAL* 4.3 2.7 - - + -
84E PRO* 3.6 24.0 - - + -
110E GLU* 3.4 8.7 - - - +
111E VAL* 2.9 67.2 + - + +
113E TYR* 3.5 32.8 - + + -
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Residues in contact with SER 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E PRO* 4.7 3.1 - - - +
22E GLN* 4.6 12.5 + - - +
27E VAL* 4.1 15.3 - - - +
28E ALA* 3.8 18.4 + - - -
58E TRP* 1.3 77.7 - - - +
60E ASP* 1.3 60.4 + - - +
61E ARG* 3.9 17.3 + - - +
108E ASP 5.7 0.3 + - - -
109E GLY 3.5 8.6 + - - -
110E GLU* 4.8 3.5 + - - +
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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