Contacts of the strand formed by residues 37 - 41 (chain E) in PDB entry 3SDI
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 THR 37 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E SER 4.6 0.4 - - - -
36E VAL* 1.3 77.5 - - - +
38E VAL* 1.3 65.4 + - - +
49E VAL 2.9 17.2 + - - -
50E ALA* 3.4 16.8 - - - +
66E LYS* 4.8 0.2 - - - -
77E SER* 3.0 28.7 + - - +
78E LEU 4.0 20.0 - - - +
79E ALA* 4.2 3.6 - - + -
137E LEU* 3.8 3.0 - - + +
164E ALA* 3.2 4.5 - - - +
165E ILE* 3.0 53.6 + - + +
197E ILE* 4.5 0.9 - - - -
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Residues in contact with VAL 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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36E VAL* 4.7 1.6 - - + -
37E THR* 1.3 82.4 + - - +
39E GLY* 1.3 66.1 + - - +
40E LEU* 4.8 6.7 - - + -
48E LEU* 3.4 4.7 - - - +
49E VAL* 2.6 46.3 + - + +
137E LEU* 3.7 4.7 - - - -
163E THR 3.4 9.9 - - - +
164E ALA* 3.8 13.5 - - + -
172E ALA* 4.0 7.4 - - + -
176E LEU* 3.9 21.1 - - + -
193E GLY* 4.6 4.0 - - - +
196E ALA* 4.3 11.0 - - + -
197E ILE* 3.8 36.1 - - + +
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Residues in contact with GLY 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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38E VAL* 1.3 77.9 - - - +
40E LEU* 1.3 61.8 + - - +
47E VAL 3.3 9.6 - - - -
48E LEU* 4.2 6.1 - - - -
137E LEU* 3.5 3.2 - - - +
148E LEU* 3.4 21.8 - - - -
162E GLY* 3.2 1.2 - - - -
163E THR 2.7 42.2 + - - +
176E LEU* 4.2 0.3 - - - +
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Residues in contact with LEU 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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38E VAL* 4.8 4.5 - - + -
39E GLY* 1.3 76.6 - - - +
41E ARG* 1.3 59.5 + - - +
46E ALA* 3.5 1.1 - - - +
47E VAL* 2.7 56.6 + - + +
49E VAL* 5.1 1.3 - - + -
139E ILE* 5.0 0.3 - - - +
148E LEU* 3.8 5.6 - - - +
161E TYR 3.4 11.4 - - - +
162E GLY* 4.2 3.1 - - - -
176E LEU* 4.1 15.3 - - + -
180E PHE* 3.7 33.2 - - + +
189E LEU* 3.6 28.5 - - + +
192E ALA* 4.3 9.2 - - + -
193E GLY* 3.7 24.7 - - - +
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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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40E LEU* 1.3 78.4 - - - +
42E SER* 1.3 92.2 + - - +
43E ASN* 3.9 14.1 + - - +
45E HIS 3.3 13.5 - - - +
46E ALA* 3.8 11.9 - - + +
146E ALA* 3.4 33.6 + - - +
147E HIS* 3.8 9.2 - - - +
148E LEU* 4.2 5.6 - - + +
159E GLU* 5.0 6.6 + - - -
160E LEU 4.4 7.8 + - - +
161E TYR* 3.0 54.1 + - - +
180E PHE* 3.6 34.3 - - - +
189E LEU* 4.5 4.5 - - - -
60F VAL* 4.3 12.3 - - - +
63F LYS* 5.9 1.2 - - - +
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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