Contacts of the strand formed by residues 21 - 28 (chain M) in PDB entry 2I2X
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 VAL 21 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M TYR* 3.7 7.0 + - + +
16M GLU 6.0 1.6 - - - +
18M THR* 3.4 33.7 + - + +
19M PHE 3.0 5.0 + - - +
20M GLY* 1.3 82.4 - - - +
22M SER* 1.3 70.5 + - - +
35M GLY 3.3 6.7 - - - +
37M GLY* 4.2 11.9 - - - +
277M LYS* 3.0 20.1 + - - -
308M ASP* 3.5 0.9 - - - -
344M LEU* 4.0 14.6 - - + -
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Residues in contact with SER 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LYS 4.9 1.0 - - - +
11M TYR* 3.4 11.0 - - - -
21M VAL* 1.3 81.9 - - - +
23M LYS* 1.3 66.4 + - - +
24M TYR* 3.3 3.5 + - - -
25M PRO* 3.7 7.2 - - - +
35M GLY* 2.9 18.3 + - - +
277M LYS* 4.0 2.7 - - - -
281M GLY 3.3 13.9 - - - -
282M MET 3.7 13.9 - - - -
283M PRO* 3.2 19.2 - - - +
308M ASP* 2.7 19.2 + - - -
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Residues in contact with LYS 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LYS* 5.2 6.5 - - - +
22G SER 5.0 0.7 - - - +
23G LYS 3.8 2.6 - - - +
25G PRO* 3.3 24.1 - - + +
33G GLU* 5.1 0.4 + - - -
36G ALA* 3.1 36.6 + - - +
37G GLY* 5.1 1.3 - - - -
10M ALA* 2.9 38.6 + - + +
11M TYR* 3.6 16.8 + - + +
22M SER* 1.3 71.2 - - - +
24M TYR* 1.3 90.2 + - + +
25M PRO* 3.2 9.0 - - - +
281M GLY* 3.0 19.4 + - - +
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Residues in contact with TYR 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G PRO* 4.0 30.5 - - + -
27G LYS* 3.4 36.3 - - + +
33G GLU* 2.8 27.4 + - + -
36G ALA* 3.9 7.8 - - + +
6M TYR* 6.3 0.7 - + - -
10M ALA* 4.5 3.8 - - + +
22M SER 4.5 1.6 - - - -
23M LYS* 1.3 112.8 + - + +
25M PRO* 1.3 68.8 - - - +
26M VAL* 4.2 2.9 - - - +
263M VAL* 4.7 1.6 - - - +
280M THR 3.2 27.1 - - - -
281M GLY 3.0 12.3 + - - +
282M MET* 4.5 8.7 - - + -
283M PRO* 3.6 19.7 - - - +
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Residues in contact with PRO 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G LYS* 3.5 22.2 - - + +
24G TYR* 3.9 29.3 - - + -
25G PRO* 4.3 4.5 - - + -
22M SER* 3.8 4.2 - - - +
23M LYS 3.2 12.6 - - - +
24M TYR* 1.3 87.2 - - - +
26M VAL* 1.3 61.2 + - - +
27M LYS* 4.3 2.5 + - + +
33M GLU* 5.8 0.4 - - + -
34M ILE 3.2 14.4 - - - +
35M GLY* 3.7 22.2 - - - +
36M ALA* 4.2 7.2 - - + -
283M PRO* 5.0 1.3 - - + -
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Residues in contact with VAL 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M TYR 4.2 1.6 - - - +
25M PRO* 1.3 76.8 - - - +
27M LYS* 1.3 63.6 + - - +
28M ALA* 4.1 5.1 + - + -
32M LEU 4.1 0.3 - - - +
33M GLU* 3.5 3.7 - - - +
34M ILE* 2.7 53.5 + - + +
160M LEU* 5.3 0.2 - - + -
213M ILE* 3.7 32.1 - - + -
263M VAL* 3.5 26.7 - - + +
264M GLY 3.2 28.3 - - - +
283M PRO* 3.8 10.5 - - + +
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Residues in contact with LYS 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G TYR* 3.7 33.8 - - + +
263G VAL* 6.1 5.2 - - + +
282G MET* 4.8 14.3 - - - +
25M PRO* 4.3 3.5 + - + +
26M VAL* 1.3 73.4 - - - +
28M ALA* 1.3 62.7 + - - +
32M LEU 3.6 4.7 - - - +
33M GLU* 3.1 34.6 + - + +
213M ILE* 2.9 19.9 - - - +
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Residues in contact with ALA 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M VAL* 4.1 3.8 + - + -
27M LYS* 1.3 77.8 - - - +
29M GLY* 1.3 69.0 + - - +
31M ASP 4.1 0.2 + - - -
32M LEU* 3.0 33.5 + - + +
34M ILE* 4.6 9.0 - - + -
121M ALA* 4.4 4.9 - - + -
159M ASP* 4.5 2.0 - - + -
160M LEU* 3.7 23.3 - - + -
213M ILE* 3.5 18.6 - - + -
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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