Contacts of the strand formed by residues 27 - 42 (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 VAL 27 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ILE* 3.8 20.6 - - + -
20E PRO* 3.1 31.9 - - + +
21E THR* 4.9 1.8 - - - -
22E GLN* 5.4 1.3 - - - -
26E PRO* 1.3 76.5 - - - +
28E ALA* 1.3 60.8 + - - +
29E VAL* 3.0 14.8 + - + +
58E TRP* 4.4 15.0 - - + -
59E SER 4.1 18.4 - - - +
82E TRP* 4.0 21.3 - - + -
149E GLU 3.0 15.1 + - - +
150E ILE* 3.8 7.1 - - + -
151E SER 3.2 18.5 + - - -
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Residues in contact with ALA 28 (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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26E PRO* 3.9 4.9 + - - -
27E VAL* 1.3 68.5 - - - +
29E VAL* 1.3 62.0 + - - +
30E SER* 3.9 1.4 + - - -
57E THR 3.8 0.2 - - - +
58E TRP* 3.4 22.6 - - - +
59E SER* 3.8 15.7 + - - -
151E SER* 4.3 6.7 - - - +
153E ASP* 5.5 3.8 - - - +
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Residues in contact with VAL 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E VAL* 3.6 20.2 - - + +
28E ALA* 1.3 72.5 - - - +
30E SER* 1.3 63.1 + - - +
31E VAL* 3.5 24.9 + - + -
56E THR* 4.5 11.9 - - + -
57E THR 3.4 9.2 - - - +
58E TRP* 4.5 6.7 - - + -
82E TRP* 5.1 0.7 - - + -
84E PRO* 4.5 16.4 - - + -
86E LEU* 4.7 2.7 - - + -
150E ILE* 3.8 23.1 - - + -
151E SER 3.0 22.8 + - - +
152E VAL* 3.4 6.4 - - + -
153E ASP* 3.1 21.9 + - - +
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Residues in contact with SER 30 (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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28E ALA 3.9 1.6 + - - -
29E VAL* 1.3 71.4 - - - +
31E VAL* 1.3 60.8 + - - +
55E GLN 3.6 4.0 - - - +
57E THR* 2.9 52.3 + - - +
153E ASP* 3.6 10.8 - - - -
155E THR* 4.3 14.6 - - - +
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E VAL* 3.5 26.5 - - + -
30E SER* 1.3 75.3 - - - +
32E SER* 1.3 84.0 + - - +
33E LEU* 4.9 4.0 - - + -
54E GLN* 4.7 15.9 - - + -
55E GLN 3.4 7.4 - - - +
56E THR* 4.6 2.9 - - + +
86E LEU* 4.2 18.8 - - + -
140E ILE* 5.1 10.5 - - + -
152E VAL* 4.4 17.9 - - + -
153E ASP 3.3 7.2 + - - +
154E PRO* 3.6 22.2 - - - +
155E THR* 4.0 5.2 - - - +
178E GLN* 3.9 1.0 - - - +
195E VAL* 4.9 14.4 - - + -
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Residues in contact with SER 32 (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* 1.3 81.7 - - - +
33E LEU* 1.3 70.2 + - - +
34E LYS* 3.9 16.3 - - - +
53E TRP 3.4 0.3 - - - +
54E GLN* 3.3 3.6 - - - -
55E GLN* 2.7 58.0 + - - -
155E THR* 5.0 13.8 + - - -
178E GLN* 3.4 21.4 + - - -
31I SER* 5.9 1.1 - - - -
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Residues in contact with LEU 33 (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* 4.9 4.7 - - + -
32E SER* 1.3 81.9 + - - +
34E LYS* 1.3 63.0 + - - +
35E PHE* 3.8 36.1 + - + -
52E PHE* 3.7 39.5 - - + -
53E TRP 3.8 1.6 - - - -
54E GLN* 3.7 22.9 - - + +
138E ILE* 4.6 19.7 - - + -
140E ILE* 4.8 12.3 - - + -
161E ASP* 4.8 1.4 - - - +
176E VAL* 4.7 3.6 - - - +
178E GLN* 3.0 26.4 + - - +
197E VAL* 4.2 15.3 - - + -
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Residues in contact with LYS 34 (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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32E SER* 3.9 15.5 - - - +
33E LEU* 1.3 73.2 - - - +
35E PHE* 1.3 64.4 - - - +
36E ILE* 3.5 7.0 + - + +
52E PHE* 3.4 2.2 - - - -
53E TRP* 3.0 46.6 + - + +
55E GLN* 3.7 22.4 - - + +
155E THR* 6.1 0.4 - - - -
159E SER* 2.3 41.4 + - - -
161E ASP* 4.3 30.1 + - + +
27I ASP 4.1 6.1 + - - -
28I ALA* 4.1 31.4 - - + +
31I SER* 5.2 9.2 + - - +
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Residues in contact with PHE 35 (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* 3.9 24.2 + - + -
34E LYS* 1.3 71.2 - - - +
36E ILE* 1.3 61.3 + - - +
38E ILE* 5.3 1.1 - - + -
50E VAL* 3.4 36.1 - - + -
52E PHE* 4.1 11.4 - + + -
138E ILE* 4.1 24.7 - - + -
161E ASP 4.6 8.2 + - - +
165E PHE* 3.3 23.5 + - + +
173E ILE* 3.7 20.5 - - + +
176E VAL* 4.1 12.8 - - + -
197E VAL* 3.7 29.2 - - + -
199E LEU* 3.7 36.6 - - + -
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Residues in contact with ILE 36 (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 5.3 7.0 - - - +
90D ASN* 6.2 2.0 - - - -
34E LYS* 3.7 13.0 - - + +
35E PHE* 1.3 72.2 - - - +
37E ASN* 1.3 67.7 + - + +
51E VAL* 2.9 25.0 + - + +
52E PHE* 3.7 2.0 - - - -
53E TRP* 3.3 61.9 - - + +
164E TYR* 5.0 21.8 - - + -
165E PHE* 2.8 21.7 - - - +
166E SER* 2.9 22.2 + - - +
28I ALA* 5.9 3.1 - - + -
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Residues in contact with ASN 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ILE* 5.6 1.4 - - + +
122D SER* 3.0 36.2 + - - -
35E PHE* 5.3 0.2 - - - +
36E ILE* 1.3 89.2 - - + +
38E ILE* 1.3 84.8 + - - +
39E LEU* 3.7 17.5 + - + +
50E VAL* 3.6 3.0 - - - -
51E VAL* 2.9 41.7 + - + +
165E PHE* 3.3 6.4 - - - -
166E SER* 3.7 16.9 - - - -
169E SER* 3.4 13.2 + - - +
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Residues in contact with ILE 38 (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* 5.3 0.7 - - + -
37E ASN* 1.3 78.0 + - - +
39E LEU* 1.3 63.4 + - - +
41E VAL* 3.8 18.4 - - + -
48E VAL* 5.0 5.8 - - + -
49E ASP 3.9 6.7 - - - +
50E VAL* 4.5 14.1 - - + +
165E PHE* 3.6 15.2 - - + -
169E SER* 2.8 24.7 + - - +
170E ARG* 4.6 1.4 + - - +
171E PHE* 3.4 30.9 - - + -
173E ILE* 4.3 14.8 - - + -
199E LEU* 3.8 18.6 - - + -
201E PHE* 3.6 37.5 - - + -
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Residues in contact with LEU 39 (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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45D THR* 5.6 3.4 - - - +
47D GLU* 4.3 25.7 - - + +
92D ILE* 4.1 24.7 - - + -
122D SER* 5.7 0.7 - - - +
37E ASN* 3.9 30.7 - - + +
38E ILE* 1.3 75.0 - - - +
40E GLU* 1.3 64.6 + - + +
41E VAL 4.1 0.2 + - - -
49E ASP* 2.8 21.4 + - + +
51E VAL* 4.1 12.3 - - + -
118E ARG* 3.4 46.9 - - - +
170E ARG* 4.2 12.0 + - - +
171E PHE* 4.0 11.6 - - - -
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Residues in contact with GLU 40 (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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39E LEU* 1.3 79.7 - - + +
41E VAL* 1.3 69.6 + - - +
47E GLU 4.5 1.1 - - - -
48E VAL* 3.5 2.6 - - - -
49E ASP* 2.9 44.2 + - + +
118E ARG* 5.6 4.0 + - - +
120E ARG* 3.0 33.0 + - - +
170E ARG* 5.2 4.7 - - - +
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Residues in contact with VAL 41 (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* 3.8 15.7 - - + -
39E LEU 4.1 0.8 + - - -
40E GLU* 1.3 81.0 - - - +
42E ASN* 1.3 66.3 + - - +
43E GLU 4.0 1.8 - - - +
47E GLU 3.7 4.9 - - - +
48E VAL* 4.7 5.4 - - + -
125E VAL* 3.4 28.0 - - + -
128E VAL* 4.1 13.2 - - + -
170E ARG* 4.8 12.8 + - - +
171E PHE* 3.2 41.3 - - + -
201E PHE* 4.3 11.0 - - + -
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Residues in contact with ASN 42 (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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41E VAL* 1.3 79.4 - - - +
43E GLU* 1.3 61.3 + - - +
44E ILE* 3.0 12.1 + - - +
45E THR* 2.5 47.7 + - - +
46E ASN* 2.9 19.6 + - - -
47E GLU* 3.1 20.9 + - + +
120E ARG* 5.3 6.0 - - - +
125E VAL* 4.3 2.7 - - - -
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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