Contacts of the helix formed by residues 55 - 69 (chain Q) in PDB entry 5IYB
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 ASP 55 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54Q PHE* 1.3 74.5 - - - +
56Q ARG* 1.3 70.5 + - - +
57Q LYS* 3.6 14.6 + - - +
58Q GLN* 3.6 30.8 + - + +
59Q LEU* 2.7 36.2 + - - +
194R ARG* 4.0 6.5 - - - +
195R PRO* 3.6 31.1 - - + +
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Residues in contact with ARG 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Q GLU* 5.3 6.6 - - + +
46Q GLU* 3.4 43.0 + - - +
49Q LEU* 3.5 37.5 - - + +
54Q PHE 3.7 2.2 + - - -
55Q ASP* 1.3 80.2 + - - +
57Q LYS* 1.3 61.8 + - - +
59Q LEU* 4.1 1.2 - - - +
60Q ARG* 3.2 53.6 + - - +
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Residues in contact with LYS 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ASN* 4.5 11.2 - - - +
297A GLY* 3.4 36.6 - - - +
55Q ASP* 3.3 12.9 + - - +
56Q ARG* 1.3 79.0 - - - +
58Q GLN* 1.3 54.5 + - - +
60Q ARG* 3.2 16.8 - - - +
61Q SER* 2.8 32.4 + - - +
27X G 2.3 40.2 + - - +
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Residues in contact with GLN 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q GLU* 5.5 2.7 - - - +
54Q PHE* 6.3 0.7 - - + -
55Q ASP* 3.5 23.8 + - + +
57Q LYS* 1.3 76.9 - - - +
59Q LEU* 1.3 58.9 + - - +
60Q ARG 3.2 1.3 - - - -
61Q SER* 3.0 15.7 + - - +
62Q VAL* 2.8 32.8 + - + +
193R ASN 4.7 0.9 - - - +
194R ARG* 2.6 33.9 + - - +
195R PRO 5.4 1.2 - - - +
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Residues in contact with LEU 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q GLU 6.0 0.4 - - - +
33Q ALA* 5.2 2.9 - - + -
45Q GLU* 5.4 2.0 - - + +
48Q MET* 4.0 3.1 - - + +
49Q LEU* 3.7 35.0 - - + +
52Q LEU* 3.8 33.4 - - + -
54Q PHE* 3.6 30.8 - - + +
55Q ASP 2.7 23.9 + - - +
56Q ARG 4.1 2.2 - - - +
58Q GLN* 1.3 71.9 - - - +
60Q ARG* 1.3 52.6 + - - +
62Q VAL* 2.9 22.6 + - + +
63Q LEU* 2.7 54.1 + - + +
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Residues in contact with ARG 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ASN 4.5 0.2 - - - -
297A GLY* 4.2 8.9 + - - -
298A ALA 3.0 22.2 - - - +
299A ALA* 3.5 31.2 + - - +
45Q GLU* 3.4 25.0 + - - +
46Q GLU* 5.7 0.2 + - - -
56Q ARG* 3.2 50.0 + - - +
57Q LYS* 3.2 20.5 - - - +
59Q LEU* 1.3 79.1 - - - +
61Q SER* 1.3 47.3 + - - -
63Q LEU* 3.2 11.0 + - + +
64Q ASN* 2.5 55.1 + - - +
96Q TYR* 4.9 5.4 - - - +
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Residues in contact with SER 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A GLN 4.0 10.4 - - - +
296A ASN* 2.8 36.0 + - - -
297A GLY 3.3 1.4 + - - -
57Q LYS* 2.8 22.3 + - - +
58Q GLN* 3.0 21.4 + - - -
60Q ARG* 1.3 74.1 - - - +
62Q VAL* 1.3 57.4 + - - +
64Q ASN* 3.5 2.0 + - - +
65Q ASN* 2.9 29.3 + - - +
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Residues in contact with VAL 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q GLU* 4.6 16.4 - - + +
30Q HIS* 3.4 47.1 - - + +
33Q ALA* 4.7 6.1 - - + -
54Q PHE* 5.7 3.4 - - + -
58Q GLN* 2.8 22.7 + - + +
59Q LEU* 3.1 24.0 - - + +
61Q SER* 1.3 75.2 - - - +
63Q LEU* 1.3 60.0 + - + +
65Q ASN* 3.2 3.3 + - - +
66Q LEU* 2.9 45.4 + - + +
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Residues in contact with LEU 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q ALA* 5.3 2.5 - - + -
45Q GLU* 4.1 14.1 - - + +
48Q MET* 3.9 32.3 - - + -
59Q LEU* 2.7 39.0 + - + +
60Q ARG* 3.2 16.4 + - - +
62Q VAL* 1.3 74.9 - - + +
64Q ASN* 1.3 58.3 + - - +
66Q LEU* 3.9 9.6 - - + +
67Q LYS* 2.8 31.8 + - - +
72Q ILE* 4.0 19.4 - - + +
96Q TYR* 3.9 41.4 - - + +
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Residues in contact with ASN 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLU* 4.1 39.6 - - + +
295A GLN* 5.9 0.4 - - - -
298A ALA* 3.8 20.9 + - - +
60Q ARG* 2.5 51.7 + - - +
61Q SER* 3.9 4.8 - - - +
63Q LEU* 1.3 72.9 - - - +
65Q ASN* 1.3 64.0 + - - +
67Q LYS* 3.9 12.1 - - - +
68Q GLY* 3.1 21.5 + - - -
96Q TYR* 5.8 0.6 + - - -
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Residues in contact with ASN 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A GLN* 5.8 6.7 + - - +
26Q TYR* 4.2 21.2 + - - -
30Q HIS* 2.8 34.8 + - - +
61Q SER 2.9 18.2 + - - +
62Q VAL* 3.6 3.6 - - - +
64Q ASN* 1.3 79.8 - - - +
66Q LEU* 1.3 59.8 + - - +
68Q GLY* 4.3 0.3 - - - -
69Q ASP* 3.5 21.0 + - - +
71Q PHE* 5.2 0.2 - - - -
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Residues in contact with LEU 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Q TYR* 4.1 16.8 - - + -
30Q HIS* 4.1 11.0 - - + +
33Q ALA* 4.3 16.6 - - + -
34Q LEU* 3.9 34.1 - - + +
37Q LEU* 5.7 0.9 - - + -
62Q VAL* 2.9 36.5 + - + +
63Q LEU* 3.9 5.8 - - + +
65Q ASN* 1.3 75.7 - - - +
67Q LYS* 1.3 60.7 + - - +
70Q LYS 3.6 3.3 + - - -
71Q PHE* 2.8 58.6 + - + +
72Q ILE* 4.0 18.2 - - + -
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Residues in contact with LYS 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LYS* 5.9 3.0 - - - +
219A GLU* 5.5 6.9 + - - -
63Q LEU 2.8 23.7 + - - +
64Q ASN* 3.9 12.6 - - - +
66Q LEU* 1.3 72.6 - - - +
68Q GLY* 1.3 60.4 + - - +
70Q LYS* 3.2 21.3 + - - +
71Q PHE 4.2 0.2 + - - -
72Q ILE* 3.8 33.1 - - + +
74Q CYS* 3.7 26.2 - - - -
96Q TYR* 5.1 7.9 - - + -
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Residues in contact with GLY 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Q ASN 3.1 16.9 + - - -
65Q ASN 4.3 0.7 - - - -
66Q LEU 3.5 0.2 - - - -
67Q LYS* 1.3 73.5 - - - +
69Q ASP* 1.3 58.9 + - - +
70Q LYS* 3.0 28.4 + - - +
226R ASP* 3.9 12.3 - - - +
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Residues in contact with ASP 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Q PHE* 5.6 0.9 - - - -
26Q TYR* 3.9 15.9 + - - +
65Q ASN* 3.5 17.4 + - - +
67Q LYS 3.6 0.2 - - - -
68Q GLY* 1.3 73.3 - - - +
70Q LYS* 1.3 62.8 + - - +
71Q PHE* 2.9 34.3 - - + -
105Q TYR* 4.9 1.6 + - - -
106Q LYS* 2.8 31.6 + - - +
223R VAL* 4.3 13.1 - - - +
224R THR* 3.7 19.8 + - - +
226R ASP* 4.5 16.2 + - - +
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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