Contacts of the strand formed by residues 40 - 48 (chain E) in PDB entry 3SGB
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 GLY 40 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E TYR* 3.5 3.2 - - - -
33E SER* 2.9 29.9 + - - +
34E SER 3.7 1.0 - - - -
39E THR* 1.3 86.4 + - - +
41E ARG* 1.3 62.1 - - - -
42E CYS* 4.3 2.0 + - - -
66E TRP* 4.8 0.3 - - - -
81E ARG* 4.1 9.7 + - - -
19I GLU* 6.0 1.6 - - - -
20I TYR 3.4 12.3 - - - -
21I ARG* 4.1 4.0 - - - -
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Residues in contact with ARG 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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30E ALA* 3.7 17.5 - - + -
31E ILE 3.3 8.7 - - - +
32E TYR* 3.7 27.7 + - + -
40E GLY* 1.3 75.0 - - - +
42E CYS* 1.3 79.0 - - - +
141E SER* 2.9 30.4 + - - +
142E THR* 2.8 28.9 + - - +
193E GLY* 3.7 6.3 - - - +
19I GLU* 3.7 1.3 - - - +
20I TYR* 2.9 81.5 + - + +
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Residues in contact with CYS 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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31E ILE* 2.8 40.4 + - + -
40E GLY 4.2 1.5 + - - -
41E ARG* 1.3 88.3 - - - +
43E SER* 1.3 59.6 + - - +
54E THR* 4.3 0.9 - - - +
58E CYS* 2.0 54.5 - - + -
66E TRP* 4.5 6.2 - - + -
141E SER* 3.4 4.9 + - - -
193E GLY 3.4 10.5 - - - -
195E SER* 3.6 6.3 - - - +
19I GLU* 4.0 16.2 - - - -
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Residues in contact with SER 43 (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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19E GLY 4.1 4.7 - - - -
29E ASP 3.3 9.0 - - - -
31E ILE* 3.8 4.9 - - - -
42E CYS* 1.3 71.8 - - - +
44E LEU* 1.3 63.7 + - - +
54E THR* 2.9 22.0 + - - -
140E GLY* 3.7 2.6 - - - -
141E SER* 2.8 25.4 + - - -
193E GLY 2.7 22.5 + - - -
194E ASP* 3.7 2.0 - - - -
195E SER 2.8 14.0 + - - -
196E GLY 3.4 5.9 - - - -
197E GLY* 3.7 18.6 - - - -
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Residues in contact with LEU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ILE* 4.0 26.0 - - + -
17E SER 3.8 21.1 - - - +
18E GLY* 3.8 5.4 - - - +
19E GLY* 2.8 27.4 + - - -
29E ASP* 2.8 17.0 + - + +
31E ILE* 3.9 16.1 - - + +
43E SER* 1.3 72.0 - - - +
45E GLY* 1.3 76.8 + - - +
46E PHE 3.9 8.3 - - - +
47E ASN* 3.9 14.6 - - - +
52E PHE* 3.8 23.3 - - + -
53E LEU 4.2 1.6 - - - -
108E TYR* 3.6 23.6 - - - +
196E GLY 3.7 0.4 - - - -
197E GLY* 3.7 0.2 - - - -
198E PRO* 3.4 5.9 - - - +
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Residues in contact with GLY 45 (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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18E GLY* 3.3 20.1 - - - -
43E SER 3.6 0.2 + - - -
44E LEU* 1.3 71.6 - - - +
46E PHE* 1.4 65.3 + - - +
53E LEU 2.6 19.6 + - - -
196E GLY 2.9 22.3 + - - -
198E PRO* 3.4 19.2 - - - +
212E LEU* 3.9 9.6 - - - -
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Residues in contact with PHE 46 (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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18E GLY* 5.0 1.3 - - - -
44E LEU* 3.9 6.7 - - - -
45E GLY* 1.4 78.5 - - - +
47E ASN* 1.3 68.3 - - - +
48E VAL* 3.7 11.4 + - + +
52E PHE* 3.3 1.9 - - - -
53E LEU* 2.8 32.5 + - + +
118E THR 5.7 2.2 - - - -
119E VAL* 3.9 18.2 - - + -
124E ILE* 4.2 16.8 - - + -
198E PRO* 3.3 24.9 - - + -
199E LEU 3.6 15.0 - - - -
200E TYR* 4.6 0.7 - - + -
209E ALA* 3.6 31.9 - - + -
211E GLY 3.3 22.2 - - - -
212E LEU* 3.8 11.7 - - + -
231E VAL* 3.9 22.0 - - + -
241E VAL* 4.7 4.9 - - + -
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Residues in contact with ASN 47 (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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16E ILE 3.2 23.4 + - - -
17E SER* 4.1 4.2 - - - +
18E GLY 5.0 1.4 - - - +
44E LEU* 3.9 5.7 - - - +
46E PHE* 1.3 75.0 - - - +
48E VAL* 1.3 62.9 + - - +
51E TYR 3.6 3.1 - - - +
52E PHE* 3.7 7.1 - - - +
108E TYR* 2.7 33.5 + - - -
115E LYS* 3.5 9.4 - - - +
116E ASP 2.6 28.8 + - - +
117E GLY* 4.8 3.4 - - - -
118E THR 5.5 2.0 + - - -
241E VAL* 4.1 8.0 - - - +
242E TYR* 3.2 34.5 + - + +
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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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46E PHE* 4.0 9.4 - - + +
47E ASN* 1.3 79.5 - - - +
48E ARG* 1.3 66.5 + - - +
50E TYR* 3.6 2.6 - - - -
51E TYR* 2.9 51.3 + - + +
52E PHE 4.5 0.2 - - - +
53E LEU* 4.0 19.1 - - + -
105E ILE* 4.3 1.1 - - + -
235E LEU* 3.8 25.1 - - + -
239E VAL* 3.6 25.8 - - + -
240E SER 3.2 13.9 - - - +
241E VAL* 4.3 8.1 - - + -
242E TYR* 3.5 7.5 - - - -
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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