Contacts of the helix formed by residues 22 - 32 (chain C) in PDB entry 2QY7
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 SER 22 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLN* 3.4 6.3 - - - +
21C TYR* 1.3 72.0 - - - +
23C GLU* 1.3 59.3 + - - +
24C ILE* 3.5 5.6 - - - +
25C GLU* 2.9 37.1 + - - +
26C SER* 3.0 31.2 + - - -
59C GLU* 3.2 20.3 + - - -
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLU* 5.2 5.4 - - - +
37A TRP* 3.9 25.2 + - - -
38A GLY* 4.9 1.9 - - - -
40A SER* 3.3 43.1 + - - +
42A GLN* 3.5 17.6 - - + +
43A LEU* 5.5 2.1 - - - +
22C SER* 1.3 74.2 - - - +
24C ILE* 1.3 59.6 + - + +
26C SER* 3.3 5.1 + - - -
27C LYS* 3.1 39.7 + - - +
56C GLN* 5.6 4.1 - - - +
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Residues in contact with ILE 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C SER* 3.5 11.2 - - - +
23C GLU* 1.3 78.0 - - - +
25C GLU* 1.3 69.0 + - - +
27C LYS* 3.2 23.9 + - + -
28C VAL* 3.0 23.9 + - + +
47C ILE* 4.6 7.9 - - + -
50C ALA* 3.5 27.4 - - + -
56C GLN* 3.9 36.8 + - + +
59C GLU* 4.0 12.6 - - + +
60C LEU* 3.6 39.0 - - + +
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ASN 4.7 0.9 - - - +
21C TYR* 3.4 19.6 - - + +
22C SER* 2.9 38.8 + - - +
24C ILE* 1.3 75.1 - - - +
26C SER* 1.3 56.5 + - - +
28C VAL* 3.4 4.0 + - - +
29C ARG* 3.0 34.9 + - - +
59C GLU* 3.8 38.9 - - + +
60C LEU* 5.6 0.2 - - - +
62C ASN* 6.1 0.2 - - - +
63C MET* 3.8 28.9 - - + +
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Residues in contact with SER 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 3.1 18.2 + - - -
21C TYR* 3.8 11.4 - - - +
22C SER 3.0 14.3 + - - -
23C GLU* 3.5 9.9 - - - -
24C ILE 3.2 0.2 - - - -
25C GLU* 1.3 76.6 - - - +
27C LYS* 1.3 56.7 + - - +
29C ARG* 3.8 9.9 - - - +
30C GLU* 2.9 30.5 + - - +
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TRP* 3.4 35.5 - - - +
23C GLU* 3.1 28.0 + - + +
24C ILE* 3.2 26.6 + - + +
26C SER* 1.3 72.8 - - - +
28C VAL* 1.3 61.8 + - - +
30C GLU* 3.4 14.4 + - - +
31C ALA* 2.9 29.6 + - - +
43C LEU* 4.3 14.4 - - + +
46C GLU* 2.6 43.6 + - + +
47C ILE* 3.6 21.2 - - + +
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.0 14.1 + - + +
25C GLU 3.7 7.0 - - - +
27C LYS* 1.3 76.4 - - - +
29C ARG* 1.3 58.6 + - - +
31C ALA* 3.3 2.9 + - - +
32C THR* 2.9 29.7 + - + +
47C ILE* 4.2 16.6 - - + -
60C LEU* 3.9 37.9 - - + +
63C MET* 3.8 11.4 - - + +
64C LEU* 3.8 35.0 - - + +
67C ARG* 4.7 4.3 - - + -
85C LEU* 4.3 9.6 - - + -
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Residues in contact with ARG 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C TYR* 3.3 57.1 + - - -
25C GLU 3.0 22.1 + - - +
26C SER* 3.8 6.4 - - - +
28C VAL* 1.3 72.8 - - - +
30C GLU* 1.3 65.7 + - - +
32C THR* 3.2 12.3 + - - -
33C ASN* 3.2 5.9 + - - +
63C MET* 3.6 27.8 - - + -
67C ARG* 3.0 50.6 + - - +
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU* 2.8 30.0 - - - +
27B LYS* 5.3 1.4 + - - -
56B GLN* 5.7 2.8 + - - -
26C SER 2.9 17.7 + - - +
27C LYS* 3.5 14.7 - - - +
29C ARG* 1.3 75.9 - - - +
31C ALA* 1.3 60.2 + - - +
32C THR 3.2 0.7 + - - -
33C ASN* 3.0 36.4 + - - +
43C LEU* 3.8 21.6 - - + +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LYS 2.9 17.4 + - - +
28C VAL 3.3 5.3 + - - +
30C GLU* 1.3 75.4 - - - +
32C THR* 1.3 59.1 + - - +
33C ASN* 3.5 1.1 - - - -
39C PRO* 3.5 33.6 - - + +
43C LEU* 3.7 21.1 - - + -
47C ILE* 3.8 15.9 - - + -
81C LYS* 3.5 15.6 + - - +
85C LEU* 4.2 11.2 - - + -
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C VAL* 2.9 18.5 + - + +
29C ARG 3.3 3.6 + - - -
30C GLU 3.1 0.6 - - - -
31C ALA* 1.3 80.5 - - - +
33C ASN* 1.3 64.2 + - - +
34C ASP* 4.7 0.3 - - - +
67C ARG* 2.8 45.0 + - + +
78C ARG* 3.5 25.9 - - - +
81C LYS* 3.9 9.2 - - - +
82C SER* 3.6 40.2 - - - +
85C LEU* 4.7 9.2 - - + -
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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