Contacts of the helix formed by residues 22 - 31 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.1 52.0 + + + -
21A HIS* 1.3 73.2 - - - +
23A GLN* 1.3 92.2 + - + +
24A PRO 3.5 0.2 - - - -
25A ALA* 3.3 4.9 + - - +
26A VAL* 3.0 27.0 + - + +
45A LEU* 3.7 25.6 - - + -
48A LEU* 3.6 30.7 - - + -
49A GLU* 3.7 43.9 + - - -
52A ARG* 4.5 10.3 - - + -
71A TYR* 5.0 1.1 - - - -
78A LEU* 4.5 1.8 - - + -
84A MET* 3.7 28.7 - - + +
92A VAL* 4.3 1.1 - - - -
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Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A HIS* 6.2 0.2 - - - -
22A PHE* 1.3 96.0 - - + +
24A PRO* 1.4 68.4 - - + +
25A ALA 3.3 0.2 + - - -
26A VAL* 3.3 1.0 + - - +
27A LYS* 3.0 54.6 + - - +
42A ASN 5.1 1.6 - - - +
45A LEU* 3.8 27.3 + - + +
46A LYS* 4.6 8.8 + - - +
49A GLU* 2.9 42.6 + - - +
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Residues in contact with PRO 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A HIS* 3.6 23.6 - - + +
23A GLN* 1.4 94.7 - - + +
25A ALA* 1.3 54.2 + - - +
27A LYS* 4.0 6.6 - - + +
28A LYS* 3.1 30.0 + - - +
92A VAL* 6.5 0.2 - - + -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A HIS 4.8 0.2 + - - -
22A PHE 3.3 6.0 + - - +
23A GLN 3.2 0.6 - - - -
24A PRO* 1.3 77.6 - - - +
26A VAL* 1.3 60.6 + - - +
28A LYS* 3.5 6.5 + - - +
29A PHE* 3.0 30.0 + - - +
84A MET* 4.3 2.2 - - + -
90A ALA* 3.4 34.5 - - + +
92A VAL* 3.5 23.5 - - + +
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.0 26.6 + - + +
23A GLN 3.8 3.4 - - - +
25A ALA* 1.3 77.0 - - - +
27A LYS* 1.3 62.7 + - - +
29A PHE* 3.1 7.0 + - - +
30A VAL* 3.0 24.1 + - + +
41A TYR* 4.2 19.5 - - + -
45A LEU* 3.8 29.8 - - + -
78A LEU* 4.0 23.1 - - + -
82A VAL* 4.2 18.2 - - + -
84A MET* 4.0 14.8 - - - -
357A PHE* 5.0 0.2 - - + -
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 3.0 51.6 + - - +
24A PRO* 4.0 5.7 - - + +
26A VAL* 1.3 75.3 - - - +
28A LYS* 1.3 62.4 + - - +
30A VAL* 3.3 9.0 - - - +
31A LEU* 3.0 38.1 + - + +
39A GLU* 4.8 4.7 - - - +
40A ALA* 3.9 21.5 - - + +
42A ASN* 3.2 28.4 + - - +
45A LEU* 3.6 19.3 - - + -
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PRO 3.1 19.3 + - - +
25A ALA* 3.7 7.6 - - - +
27A LYS* 1.3 77.3 - - - +
29A PHE* 1.3 63.0 + - - +
31A LEU* 3.7 14.4 + - - +
32A LYS* 3.8 23.3 + - + +
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA 3.0 18.1 + - - +
26A VAL 3.5 4.0 - - - +
28A LYS* 1.3 79.6 - - - +
30A VAL* 1.3 66.9 + - + +
32A LYS* 3.1 33.8 + - - +
33A ALA 4.6 0.2 + - - -
81A ARG 3.7 19.7 - - - -
82A VAL* 4.1 24.2 - - + -
83A PRO* 3.5 29.8 - - + -
89A GLU* 3.7 30.7 - - + -
90A ALA* 4.4 5.2 - - + -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.0 23.4 + - + +
27A LYS* 3.3 11.2 - - - +
29A PHE* 1.3 86.4 - - + +
31A LEU* 1.3 57.6 - - - +
32A LYS 3.0 8.9 + - - -
33A ALA* 3.6 17.8 + - - +
40A ALA* 3.5 33.2 - - + -
41A TYR* 3.9 30.3 - - + -
82A VAL* 4.8 3.1 - - + -
359A LYS* 6.4 2.2 - - - -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS* 3.0 31.9 + - + +
28A LYS* 4.1 9.6 - - - +
29A PHE 3.3 0.4 - - - -
30A VAL* 1.3 75.0 - - - +
32A LYS* 1.3 56.8 + - - +
33A ALA 3.2 10.1 + - - +
38A PRO* 3.3 30.7 - - + +
39A GLU* 5.5 1.8 - - - +
40A ALA* 4.0 15.9 - - + -
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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