Contacts of the strand formed by residues 45 - 51 (chain U) 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 CYS 45 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42U GLY* 2.8 24.3 + - - -
43U LYS 5.2 0.4 - - - -
44U ASP* 1.3 84.5 - - - +
46U THR* 1.3 68.7 + - - +
47U VAL* 4.4 4.3 - - - -
141U VAL* 3.8 4.3 - - - -
146U PRO* 3.5 8.9 - - - +
184U SER 5.1 1.8 - - - -
186U TRP* 3.7 32.5 - - + -
189U VAL* 3.8 32.8 - - - -
214U VAL* 4.4 3.4 - - + -
215U ALA 3.2 15.5 - - - +
216U THR* 4.6 4.3 - - + -
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Residues in contact with THR 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40U VAL 3.5 12.8 - - - +
41U ARG* 4.4 1.3 - - + +
42U GLY 4.7 0.2 - - - +
45U CYS* 1.3 79.7 + - - +
47U VAL* 1.3 65.6 + - - +
139U VAL* 3.6 34.2 - - + +
140U SER 3.1 23.2 + - - -
146U PRO* 3.4 13.5 - - - +
147U SER 3.4 9.0 + - - +
148U ILE* 3.8 10.5 - - + -
213U GLY 3.9 0.5 - - - +
214U VAL* 3.4 4.0 - - - +
215U ALA* 2.8 42.1 + - - +
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Residues in contact with VAL 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U LEU 3.9 0.5 - - - +
39U ALA* 3.2 5.2 - - - +
40U VAL* 2.9 35.7 + - + +
45U CYS* 4.4 3.8 - - - -
46U THR* 1.3 79.8 - - - +
48U VAL* 1.3 63.5 + - - +
49U ILE* 3.0 33.0 - - + -
139U VAL* 5.8 0.2 - - - -
186U TRP 4.4 0.4 - - - +
189U VAL* 3.6 31.4 - - + +
190U VAL* 3.7 32.5 - - + -
193U ALA* 4.1 4.3 - - + -
212U VAL* 4.3 0.9 - - + -
213U GLY 3.5 5.8 - - - +
214U VAL* 4.3 12.3 - - + -
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Residues in contact with VAL 48 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U LEU 3.3 5.2 - - - +
39U ALA* 3.5 13.7 - - + -
47U VAL* 1.3 77.2 - - - +
49U ILE* 1.3 66.3 + - - +
67U ILE* 4.4 14.3 - - + +
76U MET 5.9 0.4 - - - -
77U VAL* 4.5 26.2 - - + +
137U THR* 5.0 0.2 - - + -
139U VAL* 3.4 43.5 - - + -
211U GLU 3.8 0.5 - - - +
212U VAL* 3.4 5.4 - - - -
213U GLY* 2.9 52.4 + - - +
221U PHE* 4.6 4.9 - - + -
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Residues in contact with ILE 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37U SER* 3.0 5.7 - - - -
38U LEU* 2.8 40.6 + - + +
47U VAL* 3.0 37.5 - - + -
48U VAL* 1.3 76.9 - - - +
50U SER* 1.3 64.8 + - - +
67U ILE* 5.4 0.7 - - - -
190U VAL* 4.5 4.9 - - + +
193U ALA* 3.3 21.5 - - + +
194U ILE* 4.2 13.9 - - + -
197U MET* 3.7 29.6 - - + -
205U PHE* 6.1 0.2 - - + -
210U LEU* 4.1 20.4 - - + -
211U GLU 3.5 2.7 - - - +
212U VAL* 4.1 20.9 - - + -
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Residues in contact with SER 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35U ILE* 3.3 13.9 - - - +
36U ASN 3.3 7.4 - - - -
37U SER* 4.0 12.5 - - - -
49U ILE* 1.3 78.4 - - - +
51U GLN* 1.3 74.5 + - - +
66U TYR* 4.8 4.9 - - - +
67U ILE* 4.7 3.8 - - - -
77U VAL* 4.3 14.9 - - - +
78U VAL 5.7 0.2 + - - -
210U LEU* 3.5 8.3 - - - +
211U GLU* 3.1 45.5 + - - +
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Residues in contact with GLN 51 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34U ASN 4.6 0.6 - - - +
35U ILE* 3.5 25.7 - - + +
36U ASN* 2.6 59.3 + - - +
50U SER* 1.3 85.6 + - - +
52U LYS* 1.3 60.9 + - - +
53U LYS* 3.7 25.9 - - + +
66U TYR* 5.6 3.1 - - - -
197U MET* 4.5 5.6 - - + -
201U LEU* 3.5 20.1 - - + +
203U THR* 6.2 0.8 - - - +
205U PHE* 4.5 21.4 - - + -
209U ASP 3.4 8.5 - - - +
210U LEU* 4.3 1.8 - - + -
211U GLU* 4.5 3.5 - - - +
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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