Contacts of the helix formed by residues 22 - 33 (chain B) in PDB entry 5CRV
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 PHE 22 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.1 43.1 + + + -
21B HIS* 1.3 72.5 - - - +
23B GLN* 1.3 81.4 + - + +
24B PRO 3.4 0.4 - - - -
25B ALA* 3.2 3.6 + - - +
26B VAL* 2.9 31.6 + - + +
45B LEU* 3.6 31.0 - - + -
48B LEU* 3.6 30.5 - - + -
49B GLU* 3.3 52.5 - - + -
52B ARG* 4.5 10.3 - - + -
71B TYR* 5.1 1.8 - - - -
78B LEU* 4.5 7.6 - - + -
84B MET* 4.0 17.7 - - + -
92B VAL* 4.5 0.4 - - - -
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Residues in contact with GLN 23 (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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22B PHE* 1.3 98.1 - - + +
24B PRO* 1.4 70.1 - - + +
26B VAL* 4.0 0.2 - - - +
27B LYS* 2.9 63.7 + - - +
42B ASN* 4.6 3.5 - - - +
45B LEU* 3.8 27.8 + - + +
46B LYS* 4.3 6.2 + - - +
49B GLU* 3.7 29.9 + - - +
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Residues in contact with PRO 24 (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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21B HIS* 3.7 27.6 - - + +
22B PHE 3.7 2.7 - - - -
23B GLN* 1.4 92.8 - - + +
25B ALA* 1.3 54.9 + - - +
27B LYS* 4.2 6.6 - - + +
28B LYS* 3.1 31.6 + - - +
92B VAL* 6.0 1.6 - - + -
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Residues in contact with ALA 25 (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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21B HIS 4.3 0.8 + - - -
22B PHE 3.2 9.4 + - - +
23B GLN 3.2 0.6 - - - -
24B PRO* 1.3 78.3 - - - +
26B VAL* 1.3 60.4 + - - +
28B LYS* 3.4 7.9 + - - +
29B PHE* 2.8 30.4 + - - +
84B MET* 3.7 11.7 - - + -
90B ALA* 3.2 35.8 - - + +
92B VAL* 3.8 18.1 - - + +
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Residues in contact with VAL 26 (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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22B PHE* 2.9 23.2 + - + +
25B ALA* 1.3 75.2 - - - +
27B LYS* 1.3 58.3 + - - +
29B PHE* 3.1 8.6 + - + +
30B VAL* 2.9 37.9 + - + +
41B TYR* 5.8 3.4 - - + -
45B LEU* 3.7 38.8 - - + -
78B LEU* 4.0 20.2 - - + -
82B VAL* 4.3 25.1 - - + -
84B MET* 4.5 6.3 - - - -
357B PHE* 6.0 1.1 - - + -
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Residues in contact with LYS 27 (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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23B GLN* 2.9 53.4 + - - +
24B PRO* 4.2 4.9 - - + +
26B VAL* 1.3 75.2 - - - +
28B LYS* 1.3 56.7 + - - +
30B VAL* 3.4 9.6 + - - +
31B LEU* 2.9 38.3 + - + +
38B PRO* 5.7 2.8 - - - +
39B GLU* 5.5 6.9 + - - +
42B ASN* 3.2 34.3 + - - +
45B LEU* 4.1 12.1 - - + -
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Residues in contact with LYS 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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24B PRO 3.1 21.7 + - - +
25B ALA* 3.5 7.0 - - - +
26B VAL 3.3 0.2 - - - -
27B LYS* 1.3 72.7 - - - +
29B PHE* 1.3 56.4 + - - +
31B LEU* 3.1 10.9 + - + +
32B LYS* 2.7 46.8 + - + +
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Residues in contact with PHE 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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25B ALA 2.8 14.1 + - - +
26B VAL* 3.1 13.0 + - + +
28B LYS* 1.3 79.7 - - - +
30B VAL* 1.3 68.7 + - + +
32B LYS* 3.5 6.6 + - - +
33B ALA* 3.4 23.7 + - + +
81B ARG 4.8 5.8 - - - -
82B VAL* 4.2 20.9 - - + -
83B PRO* 3.7 33.2 - - + -
89B GLU* 3.1 35.4 - - + -
90B ALA* 4.3 8.7 - - + -
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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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26B VAL* 2.9 28.6 + - + +
27B LYS* 3.5 11.0 - - - +
29B PHE* 1.3 81.7 - - + +
31B LEU* 1.3 55.2 + - - +
33B ALA* 3.4 8.4 + - - +
35B GLY* 2.8 43.5 + - - -
38B PRO* 3.8 35.4 - - + +
41B TYR* 4.0 28.7 - - + -
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Residues in contact with LEU 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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27B LYS* 2.9 25.8 + - + +
28B LYS* 3.1 9.4 + - + +
30B VAL* 1.3 73.6 - - - +
32B LYS* 1.3 63.8 + - - +
33B ALA 3.1 1.3 - - - -
34B ALA* 3.1 14.8 + - - -
35B GLY 4.4 4.3 - - - +
38B PRO* 4.3 27.8 - - + -
39B GLU* 5.7 4.5 - - - +
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Residues in contact with LYS 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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28B LYS* 2.7 33.3 + - + +
29B PHE* 4.0 7.0 - - - +
30B VAL 3.4 0.2 - - - -
31B LEU* 1.3 72.3 - - - +
33B ALA* 1.3 55.6 + - - +
34B ALA* 3.3 2.8 + - - +
89B GLU* 4.3 28.3 + - - +
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Residues in contact with ALA 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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29B PHE* 3.4 16.9 + - + +
30B VAL* 3.4 6.0 + - - +
31B LEU 3.1 1.0 - - - -
32B LYS* 1.3 77.2 - - - +
34B ALA* 1.3 69.8 + - - +
35B GLY* 3.2 4.1 + - - -
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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