Contacts of the strand formed by residues 11 - 18 (chain T) in PDB entry 3L73
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 11 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244N ARG 3.8 2.9 - - - -
245N ASP* 2.4 39.8 + - - +
246N ASP 4.2 4.3 - - - +
247N ALA* 3.2 24.3 - - - +
248N LEU* 5.8 0.2 - - - +
237Q TYR* 4.2 6.6 - - - -
240Q PRO* 5.4 2.8 - - - +
52S GLU* 2.6 37.0 + - - -
56S ASN* 3.7 26.1 + - - +
59S MET* 5.4 3.0 - - - +
9T ARG* 4.4 21.2 - - + +
10T VAL* 1.3 82.5 - - - +
12T HIS* 1.3 99.2 + - + +
13T ILE* 3.5 12.5 + - - +
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Residues in contact with HIS 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244N ARG 2.9 15.5 + - - -
245N ASP* 4.1 12.5 - - + -
236Q ALA 3.7 0.2 - - - +
237Q TYR* 3.6 18.6 - - + -
238Q ARG* 3.0 37.8 + - - +
239Q PRO* 3.8 10.6 - - + +
240Q PRO* 3.3 37.0 - - + +
52S GLU* 5.2 0.4 - - + -
56S ASN* 4.4 12.2 + - - +
11T ARG* 1.3 113.8 + - + +
13T ILE* 1.3 58.2 + - - +
14T ILE* 4.0 3.0 + - - +
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Residues in contact with ILE 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242N ARG 3.2 3.1 - - - +
244N ARG* 3.2 29.9 + - + +
235Q MET* 4.5 2.0 - - + -
236Q ALA 3.4 8.1 - - - +
237Q TYR* 4.6 2.5 - - + -
56S ASN 5.3 0.4 - - - +
59S MET* 4.5 7.9 - - + -
60S PHE* 3.7 51.6 - - + +
63S LYS* 3.8 38.8 - - + -
10T VAL* 4.5 18.5 - - + +
11T ARG 3.5 11.3 - - - +
12T HIS* 1.3 81.6 - - - +
14T ILE* 1.3 70.9 + - - +
15T THR* 4.4 3.7 - - + +
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Residues in contact with ILE 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152N TYR* 4.5 9.2 - - - +
241N ILE* 4.0 20.9 - - + -
242N ARG 3.2 10.5 - - - +
243N ALA* 4.5 10.3 - - + -
235Q MET* 3.2 1.4 - - - +
236Q ALA* 2.9 37.9 + - + +
238Q ARG* 4.0 32.1 - - + +
5R VAL* 4.3 16.2 - - + -
12T HIS 4.6 5.6 - - - +
13T ILE* 1.3 77.4 - - - +
15T THR* 1.3 72.4 + - - +
16T TYR* 3.7 29.6 - - + +
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Residues in contact with THR 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240N GLU* 3.9 2.6 + - - +
241N ILE* 3.1 8.0 + - - +
242N ARG* 3.0 53.7 + - - +
233Q ARG* 4.4 20.6 - - - +
234Q LYS 3.2 6.3 - - - +
235Q MET* 3.6 19.5 - - + -
63S LYS* 4.3 20.6 - - - +
13T ILE* 4.4 2.7 - - + +
14T ILE* 1.3 83.2 - - - +
16T TYR* 1.3 65.1 + - - +
17T SER* 5.0 2.2 - - - -
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Residues in contact with TYR 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240N GLU 3.5 6.7 - - - +
241N ILE* 4.1 24.2 - - + -
233Q ARG* 3.6 1.9 - - - +
234Q LYS* 2.8 45.6 + - + -
235Q MET 4.9 0.4 - - - -
236Q ALA* 4.7 15.7 - - + +
238Q ARG* 5.3 3.6 + - - -
5R VAL* 3.8 12.1 - - + +
6R THR 3.7 16.1 + - - -
7R VAL* 3.8 20.4 - - + -
8R PRO* 3.5 36.1 - - + -
10R PHE* 3.8 23.5 - - + -
14T ILE* 3.7 32.1 - - + +
15T THR* 1.3 77.5 - - - +
17T SER* 1.3 65.9 + - - +
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Residues in contact with SER 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239N SER* 2.9 21.7 - - - -
240N GLU* 3.1 35.8 + - - +
434N TYR* 5.5 0.9 - - - -
229Q VAL* 3.9 28.5 + - - +
230Q LEU* 6.0 0.2 - - - +
232Q SER* 5.6 0.4 - - - -
233Q ARG* 3.6 21.8 - - - +
10R PHE* 4.4 4.7 - - - -
15T THR* 5.0 2.3 - - - -
16T TYR* 1.3 79.5 + - - +
18T LEU* 1.3 66.5 + - - +
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Residues in contact with LEU 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159N GLN* 3.7 21.5 - - - +
237N THR* 3.9 5.2 - - + -
238N GLY 3.8 4.3 - - - +
239N SER* 3.5 20.2 - - - -
434N TYR* 4.9 2.7 - - - -
229Q VAL* 3.5 13.3 + - - +
232Q SER* 5.0 3.2 + - - -
10R PHE* 3.5 48.0 - - + +
13R TYR* 5.7 0.4 - - + -
14R ARG* 4.2 22.7 - - + +
17T SER* 1.3 77.0 - - - +
19T SER* 1.3 72.0 + - - +
22T GLU* 4.6 13.7 - - + +
23T GLN* 3.0 30.6 + - + +
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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