Contacts of the helix formed by residues 44 - 53 (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 LYS 44 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42Q CYS 3.9 1.4 + - - -
43Q VAL* 1.3 74.1 - - - +
45Q GLU* 1.3 58.0 + - - +
46Q GLU* 2.7 44.3 + - + +
47Q ASP* 2.9 17.1 + - + +
48Q MET* 2.6 33.4 + - - +
77Q ARG* 5.4 13.2 - - - +
93Q PHE* 3.6 38.1 - - + -
94Q ILE 4.5 8.3 - - - +
95Q ASN* 5.2 2.0 - - - +
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Residues in contact with GLU 45 (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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43Q VAL 3.6 2.9 + - - -
44Q LYS* 1.3 74.1 - - - +
46Q GLU* 1.3 64.5 + - - +
48Q MET* 3.3 8.2 + - + +
49Q LEU* 2.7 33.7 + - + +
56Q ARG* 5.3 6.0 - - + +
59Q LEU* 5.4 2.2 - - + +
60Q ARG* 3.4 37.1 + - - +
63Q LEU* 4.1 12.3 - - + +
94Q ILE* 3.8 29.9 + - + +
96Q TYR* 3.3 45.4 + - + -
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Residues in contact with GLU 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Q LYS* 2.7 41.6 + - + +
45Q GLU* 1.3 84.6 + - - +
47Q ASP* 1.3 57.5 + - - +
49Q LEU* 3.3 9.0 + - - +
50Q GLU* 3.0 27.8 + - - +
56Q ARG* 3.4 38.4 + - - +
93Q PHE* 5.7 0.2 - - - -
94Q ILE* 5.6 1.0 - - - +
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Residues in contact with ASP 47 (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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43Q VAL* 4.4 14.7 - - + +
44Q LYS* 2.9 27.3 + - + +
46Q GLU* 1.3 78.5 - - - +
48Q MET* 1.3 59.4 + - - +
49Q LEU 3.1 0.2 - - - -
50Q GLU* 3.8 10.9 - - - +
51Q LEU* 2.8 38.5 + - - +
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Residues in contact with MET 48 (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* 4.3 5.2 - - + +
36Q ILE* 3.7 21.8 - - + -
37Q LEU* 3.6 34.1 - - + -
43Q VAL* 3.8 25.5 - - + +
44Q LYS 2.6 18.1 + - - +
45Q GLU* 3.5 8.3 - - + +
47Q ASP* 1.3 72.9 - - - +
49Q LEU* 1.3 57.5 + - - +
51Q LEU* 4.0 6.1 - - + -
52Q LEU* 3.1 48.3 + - + +
59Q LEU* 4.4 3.4 - - + -
63Q LEU* 3.9 32.3 - - + -
96Q TYR* 4.6 17.7 - - + -
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Residues in contact with LEU 49 (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* 2.7 14.6 + - + +
46Q GLU* 3.3 10.8 - - - +
47Q ASP 3.1 0.2 - - - -
48Q MET* 1.3 75.3 - - - +
50Q GLU* 1.3 55.5 + - - +
52Q LEU 3.6 0.3 - - - -
53Q LYS* 2.6 36.0 + - - -
54Q PHE 3.2 27.1 - - - +
56Q ARG* 3.5 63.0 - - + +
59Q LEU* 3.7 22.2 - - + -
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Residues in contact with GLU 50 (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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46Q GLU 3.0 15.8 + - - +
47Q ASP* 3.3 11.7 + - - +
49Q LEU* 1.3 75.6 - - - +
51Q LEU* 1.3 59.9 + - - +
53Q LYS* 2.6 51.2 + - + +
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Residues in contact with LEU 51 (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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36Q ILE* 4.6 27.8 - - + -
43Q VAL* 5.3 12.1 - - + -
47Q ASP* 2.8 26.2 + - - +
48Q MET* 4.1 6.7 - - - +
50Q GLU* 1.3 78.2 - - - +
52Q LEU* 1.3 64.5 + - + +
53Q LYS* 4.3 6.6 + - - +
163R LEU* 3.5 58.0 - - + +
164R GLY* 5.9 0.5 - - - -
203R PHE* 6.0 0.3 - - - -
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Residues in contact with LEU 52 (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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32Q LEU* 3.9 24.5 - - + +
33Q ALA* 4.5 6.5 - - + -
36Q ILE* 3.6 37.9 - - + -
48Q MET* 3.1 32.7 + - + +
49Q LEU 4.0 1.1 - - - +
51Q LEU* 1.3 82.5 - - + +
53Q LYS* 1.3 66.0 + - - +
54Q PHE* 3.1 36.7 + - + +
59Q LEU* 3.8 28.5 - - + -
201R LEU* 3.7 8.0 - - - +
203R PHE* 3.9 8.7 - - - -
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Residues in contact with LYS 53 (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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49Q LEU 2.6 18.3 + - - -
50Q GLU* 2.6 39.4 + - + +
51Q LEU* 3.4 6.5 + - - +
52Q LEU* 1.3 74.1 - - - +
54Q PHE* 1.3 63.6 + - - +
164R GLY* 5.6 6.5 + - - +
166R ILE* 4.8 19.1 - - + -
194R ARG* 3.4 12.8 - - - +
195R PRO* 3.8 9.4 - - - +
201R LEU* 3.5 25.2 - - + +
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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