Contacts of the helix formed by residues 40 - 51 (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 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLU* 3.2 26.7 + - - +
26B SER* 6.0 2.0 - - - -
27B LYS* 4.2 7.9 - - - -
30B GLU* 5.7 1.6 - - - -
37C TRP* 3.8 30.2 - - - -
38C GLY* 3.9 2.8 - - - -
39C PRO* 1.3 76.9 - - - +
41C GLY* 1.3 65.0 + - - +
42C GLN* 3.8 5.6 + - - -
43C LEU* 3.0 20.3 + - - +
44C MET* 3.1 22.7 + - - +
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Residues in contact with GLY 41 (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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30B GLU* 5.8 1.0 + - - -
39C PRO 3.8 1.0 + - - -
40C SER* 1.3 72.6 - - - +
42C GLN* 1.3 56.5 + - - +
44C MET* 3.4 16.3 + - - +
45C GLY* 2.9 26.0 + - - -
88C TYR* 4.1 9.8 + - - -
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Residues in contact with GLN 42 (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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36A PRO* 4.1 14.3 - - - +
37A TRP* 4.7 1.4 - - - -
20B ASN* 5.3 4.9 + - - +
21B TYR 3.4 22.2 + - - +
23B GLU* 3.6 23.1 - - - +
26B SER* 3.7 25.1 + - - +
40C SER* 3.2 5.1 + - - +
41C GLY* 1.3 75.2 - - - +
43C LEU* 1.3 57.0 + - - +
45C GLY* 3.3 3.8 + - - -
46C GLU* 3.0 59.9 + - - +
49C LYS* 6.1 0.4 - - - +
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Residues in contact with LEU 43 (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* 3.8 28.0 - - - +
27C LYS* 4.3 20.2 - - + +
30C GLU* 3.8 28.3 - - + +
31C ALA* 3.7 35.4 - - + -
39C PRO* 4.2 8.3 - - + -
40C SER* 3.0 23.7 + - - +
42C GLN* 1.3 73.3 - - - +
44C MET* 1.3 65.2 + - - +
46C GLU* 3.2 19.0 + - - +
47C ILE* 3.1 30.0 + - + +
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Residues in contact with MET 44 (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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31C ALA* 5.6 0.2 - - + -
39C PRO* 3.7 44.4 - - + +
40C SER 3.1 16.8 + - - +
41C GLY* 3.8 12.6 - - - +
43C LEU* 1.3 75.2 - - - +
45C GLY* 1.3 57.0 + - - +
47C ILE* 3.5 2.5 + - - +
48C ALA* 2.9 23.9 + - - +
84C LEU* 4.0 14.8 - - - +
85C LEU* 3.9 19.7 - - + -
88C TYR* 3.4 56.9 - - + -
89C LEU* 4.2 1.6 - - - +
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Residues in contact with GLY 45 (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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41C GLY 2.9 13.0 + - - -
42C GLN* 3.3 6.0 + - - -
43C LEU 3.2 0.2 - - - -
44C MET* 1.3 77.8 - - - +
46C GLU* 1.3 55.3 + - - +
48C ALA* 3.4 3.8 + - - +
49C LYS* 3.0 35.5 + - - +
88C TYR* 3.6 19.9 - - - -
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Residues in contact with GLU 46 (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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36A PRO 4.2 1.2 - - - +
37A TRP* 3.5 42.7 - - + +
23B GLU* 4.1 14.9 + - - +
27C LYS* 2.6 40.3 + - + +
42C GLN* 3.0 44.9 + - - +
43C LEU* 3.2 20.5 + - - +
45C GLY* 1.3 72.1 - - - +
47C ILE* 1.3 67.0 + - - +
49C LYS* 3.2 12.2 + - - +
50C ALA* 3.1 21.3 + - - +
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Residues in contact with ILE 47 (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* 4.6 3.4 - - + -
27C LYS* 3.6 43.5 - - + +
28C VAL* 4.1 6.3 - - + +
31C ALA* 3.8 19.7 - - + -
43C LEU* 3.1 20.1 + - + +
44C MET 3.8 4.3 - - - +
45C GLY 3.4 0.2 - - - -
46C GLU* 1.3 73.9 - - - +
48C ALA* 1.3 63.8 + - - +
50C ALA* 3.0 18.3 + - - +
51C THR* 3.1 13.0 + - - +
60C LEU* 3.8 30.1 - - + -
85C LEU* 4.0 18.2 - - + -
89C LEU* 3.9 16.2 - - + -
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Residues in contact with ALA 48 (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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44C MET 2.9 18.8 + - - +
45C GLY* 3.5 6.1 - - - +
46C GLU 3.3 0.2 - - - -
47C ILE* 1.3 74.3 - - - +
49C LYS* 1.3 62.9 + - + +
51C THR* 2.6 23.6 + - - -
52C PHE* 3.2 11.7 - - - -
88C TYR* 4.0 13.5 - - + -
89C LEU* 3.5 19.8 - - + +
92C ASN* 4.0 22.4 - - + +
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Residues in contact with LYS 49 (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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35A ASP* 5.6 2.2 + - - -
36A PRO* 5.3 1.4 - - - +
37A TRP* 3.8 35.7 - - + -
20B ASN* 4.4 19.4 + - - +
42C GLN* 6.1 0.4 - - - +
45C GLY 3.0 19.7 + - - +
46C GLU* 3.2 9.6 + - + +
48C ALA* 1.3 76.0 - - + +
50C ALA* 1.3 62.8 + - - +
52C PHE* 3.2 26.4 + - - +
53C MET* 4.0 14.2 + - + +
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Residues in contact with ALA 50 (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* 3.5 30.1 - - + -
27C LYS* 5.9 0.2 - - + -
46C GLU 3.1 10.0 + - - +
47C ILE 3.0 10.2 + - - +
49C LYS* 1.3 71.6 - - - +
51C THR* 1.3 57.5 + - - +
52C PHE 3.1 5.6 - - - -
53C MET* 3.0 39.9 + - - +
56C GLN* 3.8 18.7 - - + +
57C PHE 4.3 1.0 + - - -
60C LEU* 3.7 5.2 - - + -
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Residues in contact with THR 51 (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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47C ILE 3.1 14.7 + - - +
48C ALA 2.6 17.8 + - - +
50C ALA* 1.3 74.7 - - - +
52C PHE* 1.3 57.2 + - - +
53C MET 3.4 0.2 - - - -
54C TYR* 5.5 0.2 - - - -
57C PHE* 3.6 26.5 - - + +
60C LEU* 3.6 23.6 - - + -
89C LEU* 4.0 15.5 - - + -
93C GLY* 3.4 1.4 - - - -
94C SER* 2.8 44.5 + - - -
96C ARG* 5.1 2.6 + - - -
97C VAL* 3.8 20.0 - - + -
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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