Contacts of the strand formed by residues 27 - 34 (chain B) in PDB entry 4ICX
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 MSE 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B PRO 5.9 1.6 - - - +
25B LYS 5.8 0.7 - - - -
26B HIS* 1.3 94.9 - - - +
28B LEU* 1.3 65.1 + - - +
43B PRO* 3.9 26.5 - - + +
44B VAL* 3.1 16.6 - - - +
45B ASP* 2.8 45.8 - - - +
46B HIS* 4.0 4.9 - - - -
81B ALA* 3.3 7.3 - - - -
82B LEU* 2.8 39.1 + - + +
84B PRO* 3.6 26.7 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.7 20.0 - - + -
27B MSE 1.3 73.4 - - - +
29B VAL* 1.3 62.1 + - - +
42B ASP 3.7 1.6 - - - +
43B PRO* 3.3 4.2 - - - +
44B VAL* 2.8 44.6 + - + +
46B HIS* 3.5 35.2 - - + +
50B PRO* 3.6 35.0 - - + -
52B PHE* 3.8 14.1 - - + -
79B CYS* 3.7 19.1 - - - -
80B PHE 3.3 16.2 - - - +
92B ILE* 3.9 9.4 - - + -
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 1.3 80.3 - - - +
30B VAL* 1.3 70.8 + - - +
31B GLU* 4.2 16.8 - - + +
40B ALA* 4.5 4.7 - - + -
41B THR* 3.8 22.9 - - - +
43B PRO* 3.9 26.0 - - + -
78B GLN 3.7 1.0 - - - +
79B CYS* 3.5 2.6 - - - -
80B PHE* 2.7 42.4 + - + +
82B LEU* 4.2 21.3 - - + -
89B LYS* 5.1 7.2 - - - -
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 3.9 11.2 - - + -
29B VAL* 1.3 74.4 - - - +
31B GLU* 1.3 64.5 + - - +
32B ALA 3.9 0.9 + - - +
40B ALA* 3.6 1.6 - - - -
41B THR* 3.1 42.3 + - + +
52B PHE* 3.6 32.3 - - + -
56B LEU* 4.8 1.2 - - - +
77B LEU* 3.7 40.8 - - + -
78B GLN 3.4 7.6 - - - +
79B CYS* 4.3 8.7 - - + +
95B ILE* 6.3 0.2 - - + -
126B ILE* 4.2 16.2 - - + -
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 4.1 6.7 - - + +
30B VAL* 1.3 74.8 - - - +
32B ALA* 1.3 60.6 + - - +
33B LYS* 5.3 1.0 - - - +
38B GLN* 3.0 35.4 + - - +
39B LEU 3.4 4.3 - - - -
40B ALA* 4.1 13.2 - - + +
76B LYS 3.6 2.1 - - - +
77B LEU* 3.5 1.0 - - - -
78B GLN* 2.8 39.6 + - + +
80B PHE* 3.5 30.7 - - + -
89B LYS* 2.5 32.7 + - - -
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 5.9 0.4 - - + -
30B VAL* 3.9 1.2 + - + +
31B GLU* 1.3 72.6 - - - +
33B LYS* 1.3 61.2 + - - +
38B GLN* 3.4 3.3 - - - +
39B LEU 2.7 40.4 + - - +
56B LEU* 3.6 28.0 - - + -
58B TRP* 3.6 22.3 - - + -
75B ILE* 4.6 0.2 - - + -
76B LYS 3.5 3.6 - - - -
77B LEU* 4.1 21.3 - - + +
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 5.6 9.6 - - - +
53A ALA* 6.0 5.6 - - - -
31B GLU 5.3 1.1 - - - +
32B ALA* 1.3 75.5 - - - +
34B PHE* 1.3 63.5 + - - +
35B ASP 4.3 0.4 - - - +
36B GLY* 3.7 28.4 + - - +
37B GLU 3.8 6.1 - - - +
38B GLN* 3.4 36.8 + - + +
58B TRP* 4.2 1.1 - - - -
74B PRO 4.1 1.6 - - - +
75B ILE* 3.7 1.9 - - - +
76B LYS* 3.0 42.5 + - + +
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Residues in contact with PHE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.7 17.5 - - + -
33B LYS* 1.3 75.1 - - - +
35B ASP* 1.3 79.4 + - + +
36B GLY 3.1 2.0 + - - -
37B GLU* 3.1 22.7 + - - +
58B TRP* 3.8 37.8 + + + +
60B ILE* 3.9 17.0 - - + -
68B HIS* 3.6 24.9 - + - -
73B THR* 3.7 20.4 - - + -
74B PRO 3.4 17.0 - - - -
75B ILE* 3.7 22.9 - - + -
99B LEU* 3.8 26.0 - - + -
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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