Contacts of the strand formed by residues 32 - 37 (chain I) in PDB entry 4EUP
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 PHE 32 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I TYR* 3.4 41.3 - + - -
29I SER* 3.7 20.6 - - - -
30I GLN* 3.8 19.7 - - - -
31I SER* 1.3 75.3 - - - +
33I PHE* 1.3 67.5 + - - +
34I TRP* 5.9 0.2 - - - -
48I SER* 3.3 4.9 - - - -
49I ILE* 3.0 50.3 + - + +
50I TYR* 4.6 0.4 - - - -
64I LEU* 3.5 33.9 - - + -
66I LYS* 4.6 3.8 - - + -
71I VAL* 3.6 23.6 - - + -
88I CYS* 6.1 0.9 - - - -
89I ALA 3.8 3.6 - - - +
90I VAL* 3.6 31.4 - - + -
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Residues in contact with PHE 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I SER* 3.7 33.2 - - - -
32I PHE* 1.3 78.4 - - - +
34I TRP* 1.3 66.8 + - - +
35I TYR* 3.8 23.8 - + + -
45I LEU* 4.0 10.5 - - + -
47I MET 3.2 6.1 - - - +
48I SER* 3.2 33.0 - - - -
50I TYR* 3.9 11.9 - + - -
88I CYS* 3.5 7.3 - - - -
89I ALA* 2.9 42.9 + - + +
91I SER* 4.0 0.9 - - - -
98I LEU* 3.6 34.8 - - + -
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Residues in contact with TRP 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I GLN* 3.4 24.7 - - - -
20I LEU* 3.9 30.1 - - + -
21I ASN 3.9 2.5 - - - -
22I CYS* 3.9 21.3 - - + -
33I PHE* 1.3 76.5 - - - +
35I TYR* 1.3 62.7 + - - +
45I LEU* 3.8 2.3 - - - +
46I ILE* 2.9 29.4 + - + +
47I MET* 2.8 42.5 + - + +
49I ILE* 5.5 2.7 - - + -
62I ALA* 4.5 1.3 - - + +
71I VAL* 3.7 24.4 - - + +
72I SER 3.2 35.9 + - - -
73I LEU* 3.5 32.7 - - + +
86I TYR* 4.6 8.7 - - + -
87I LEU 3.3 19.5 - - - -
88I CYS* 3.6 8.3 - - + -
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Residues in contact with TYR 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I PHE* 3.8 22.8 - + + +
34I TRP* 1.3 77.4 - - - +
36I ARG* 1.3 60.8 + - - +
43I PRO* 4.1 26.7 - - + -
44I GLU 2.9 22.7 - - - +
45I LEU* 3.6 27.8 - - + +
46I ILE* 4.3 2.5 - - - -
85I THR 3.7 0.5 - - - +
86I TYR* 3.3 3.3 - - - -
87I LEU* 2.6 52.6 + - + +
89I ALA* 3.8 17.9 - - + -
98I LEU* 3.7 17.8 - - + +
100I PHE* 4.0 22.0 - + - -
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Residues in contact with ARG 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I TYR* 1.3 71.7 - - - +
37I GLN* 1.3 62.3 + - - +
38I TYR* 3.4 42.5 + - + -
42I SER 4.0 1.0 - - - +
43I PRO* 3.6 0.4 - - - -
44I GLU* 2.7 73.2 + - - +
46I ILE* 3.8 23.3 - - + +
60I PHE* 4.1 20.2 - - - -
81I SER 4.7 3.2 + - - -
82I ASP* 4.7 7.5 + - - -
84I ALA* 3.5 17.5 - - + -
85I THR 3.5 3.6 - - - -
86I TYR* 3.6 33.2 + - + -
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Residues in contact with GLN 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I ARG* 1.3 75.3 - - - +
38I TYR* 1.3 65.8 + - - +
39I SER 3.9 0.3 + - - -
40I GLY 5.9 0.4 - - - +
41I LYS 2.9 29.4 + - - +
42I SER* 3.4 13.9 - - - +
43I PRO* 3.8 20.9 - - + +
84I ALA* 3.9 2.4 - - - -
85I THR* 2.8 45.9 + - - +
87I LEU* 3.5 23.2 - - + +
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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