Contacts of the strand formed by residues 49 - 54 (chain E) in PDB entry 4GOM
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 ARG 49 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E GLU* 3.0 56.4 + - - +
30E CYS* 3.1 23.8 - - + +
31E LEU 2.8 24.3 + - - -
47E PHE* 3.1 4.2 - - - +
48E SER* 1.3 86.1 + - - +
50E TYR* 1.3 70.0 + - - +
51E ILE* 6.2 0.4 - - - +
157E ASN* 3.4 13.9 - - + +
173E ASP* 4.5 11.1 + - - -
175E ALA* 4.1 12.3 - - - +
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Residues in contact with TYR 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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30E CYS* 4.4 1.3 - - - -
31E LEU* 3.4 36.1 - - + -
42E PHE* 3.4 43.6 + + - -
45E THR* 2.6 39.4 + - - -
47E PHE* 3.1 35.4 + + + -
49E ARG* 1.3 81.0 - - - +
51E ILE* 1.3 64.0 + - - +
52E LEU* 4.0 13.2 - - + -
154E LYS* 3.5 11.2 + - + -
157E ASN* 2.9 21.1 + - + +
158E ALA* 3.3 13.0 - - + -
159E PHE* 2.9 28.1 + - - +
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Residues in contact with ILE 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E CYS* 3.6 24.0 - - - -
31E LEU 2.9 10.6 + - - +
32E VAL* 3.3 23.6 - - + -
33E GLU 2.9 26.9 + - - +
49E ARG* 6.1 0.2 - - + -
50E TYR* 1.3 72.2 - - - +
52E LEU* 1.3 65.3 + - - +
159E PHE* 3.6 12.8 - - + -
161E TYR* 4.1 28.5 - - + +
168E SER* 5.1 6.1 - - - -
171E ARG* 4.1 31.6 - - + +
176E SER* 6.0 0.2 - - - +
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Residues in contact with LEU 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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31E LEU 4.8 0.4 - - - +
33E GLU* 3.7 34.1 - - + +
36E VAL* 4.3 15.0 - - + -
42E PHE* 3.4 45.8 - - + -
50E TYR* 4.1 17.0 - - + -
51E ILE* 1.3 79.7 - - - +
53E ALA* 1.4 60.7 + - - +
60E ILE* 4.3 0.7 - - - +
158E ALA* 4.2 5.2 - - + -
159E PHE 2.8 11.2 + - - +
160E PHE* 3.0 41.0 - - + +
161E TYR 2.9 23.0 + - - +
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Residues in contact with ALA 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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33E GLU 2.9 11.0 + - - +
34E PRO 3.1 10.6 - - - +
36E VAL* 3.0 29.1 + - - +
51E ILE* 5.3 1.6 - - + -
52E LEU* 1.4 73.0 - - - +
54E ASP* 1.3 61.4 - - - +
60E ILE* 4.3 0.9 - - - -
161E TYR* 3.1 19.1 - - + +
163E GLU* 4.5 8.5 - - + +
168E SER* 3.5 34.8 - - - +
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Residues in contact with ASP 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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34E PRO 4.1 0.2 - - - -
36E VAL* 3.9 4.7 + - + -
37E GLY 3.1 17.8 + - - -
53E ALA* 1.3 77.1 - - - +
55E ILE* 1.3 67.3 + - - +
56E ASN* 3.1 17.9 + - - +
59E LEU* 3.4 21.0 - - + +
60E ILE* 3.8 12.1 - - + +
161E TYR 3.2 3.1 + - - +
162E CYS* 3.1 26.0 - - - -
163E GLU 3.2 6.8 + - - -
301E 0Y0 2.9 55.5 + - - +
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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