Contacts of the helix formed by residues 19 - 29 (chain H) in PDB entry 2QXU
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 19 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8H MET* 3.3 47.3 - - + -
9H VAL 3.5 25.1 - - - -
10H HIS* 3.5 30.5 - - + -
15H ALA 4.6 3.4 - - - -
16H SER* 3.3 17.1 + - - +
17H PHE 3.0 1.6 - - - -
18H ASN* 1.3 81.4 - - + +
20H ALA* 1.3 57.0 + - - +
21H GLY 3.3 2.0 - - - -
22H ILE* 3.3 20.3 + - + -
23H LYS* 2.8 34.1 + - - +
38H ALA* 4.5 4.0 - - + -
74H VAL* 3.9 21.1 - - + -
76H HIS* 4.2 11.9 - - + -
102H LEU* 4.7 2.0 - - + -
160H LEU* 4.4 15.9 - - + -
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Residues in contact with ALA 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H SER 4.5 0.4 + - - -
17H PHE* 3.1 20.3 + - + +
18H ASN 3.4 1.4 - - - -
19H PHE* 1.3 76.0 - - - +
21H GLY* 1.3 64.0 + - - +
23H LYS* 3.4 7.7 + - - +
24H SER* 3.1 27.3 + - - -
33H ARG* 5.1 1.1 + - - +
161H TYR* 4.2 7.0 - - + +
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Residues in contact with GLY 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H PHE 3.3 0.4 - - - -
20H ALA* 1.3 79.4 - - - +
22H ILE* 1.3 62.3 + - - +
24H SER* 3.5 5.5 + - - -
25H TYR* 3.1 23.4 + - - +
160H LEU 4.6 0.2 - - - -
161H TYR* 3.3 32.5 - - - -
166H ASN* 4.9 3.0 + - - -
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Residues in contact with ILE 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H MET* 4.1 15.7 - - + -
19H PHE* 3.3 27.3 + - + +
21H GLY* 1.3 72.6 - - - +
23H LYS* 1.3 60.8 + - - +
25H TYR* 3.4 6.4 + - + +
26H LEU* 3.0 38.7 + - + +
74H VAL* 4.8 9.4 - - + -
102H LEU* 5.1 7.4 - - + -
159H LEU 4.4 7.9 - - - +
160H LEU* 3.3 32.1 - - + +
165H VAL* 5.3 0.9 - - + -
166H ASN* 3.0 30.3 - - - +
169H ILE* 4.4 18.8 - - + -
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Residues in contact with LYS 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H MET* 4.0 23.7 - - + +
16H SER 5.2 1.8 + - - -
19H PHE* 2.8 18.7 + - - +
20H ALA* 3.6 7.2 - - - +
22H ILE* 1.3 74.9 - - - +
24H SER* 1.3 65.2 + - - +
26H LEU 3.4 0.7 + - - -
27H VAL* 3.1 27.8 + - - +
33H ARG* 3.4 31.9 - - - +
36H LEU* 3.4 52.0 + - + +
38H ALA* 3.9 22.8 - - - +
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Residues in contact with SER 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H ALA 3.1 17.3 + - - -
21H GLY* 3.5 5.8 + - - -
23H LYS* 1.3 75.8 - - - +
25H TYR* 1.3 62.0 + - - +
27H VAL* 3.3 4.3 + - - +
28H SER* 3.0 22.5 + - - -
33H ARG* 3.7 23.8 + - - +
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Residues in contact with TYR 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H GLY 3.1 19.0 + - - +
22H ILE* 3.6 6.3 - - + +
24H SER* 1.3 77.3 - - - +
26H LEU* 1.3 77.7 + - + +
28H SER* 2.5 29.2 + - - -
29H GLN* 3.1 35.4 + - + +
163H SER 5.4 0.7 - - - -
166H ASN* 3.2 63.4 + - + +
167H SER* 3.6 11.8 + - - -
169H ILE* 5.5 0.4 - - + -
170H LYS* 3.6 29.0 - - + +
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Residues in contact with LEU 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H VAL* 4.8 0.4 - - + -
8H MET* 3.7 29.8 - - + -
22H ILE* 3.0 24.3 + - + +
23H LYS 3.8 3.8 - - - +
25H TYR* 1.3 95.3 - - + +
27H VAL* 1.3 60.7 + - - +
29H GLN* 3.0 8.2 + - - +
30H GLY 3.3 0.5 + - - -
31H TRP* 2.9 58.3 + - + +
36H LEU* 4.1 14.6 - - + -
74H VAL* 5.1 0.4 - - + -
169H ILE* 4.0 9.2 - - + -
170H LYS* 4.7 1.8 - - - -
173H LEU* 3.6 33.0 - - + -
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Residues in contact with VAL 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H LYS 3.1 16.1 + - - +
24H SER* 3.5 9.2 - - - +
25H TYR 3.2 0.2 - - - -
26H LEU* 1.3 75.9 - - - +
28H SER* 1.3 63.3 + - - +
30H GLY* 3.1 12.1 + - - -
31H TRP 3.3 20.8 - - - +
33H ARG* 3.8 42.0 - - + +
36H LEU* 3.9 12.6 - - + -
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Residues in contact with SER 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H SER 3.0 13.8 + - - -
25H TYR* 2.5 27.3 + - - -
27H VAL* 1.3 77.8 - - - +
29H GLN* 1.3 76.0 + - - +
30H GLY 3.4 0.8 + - - -
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Residues in contact with GLN 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H HIS* 4.8 3.1 - - - -
25H TYR* 3.4 46.7 - - + +
26H LEU* 3.0 10.3 + - - +
28H SER* 1.3 98.4 + - - +
30H GLY* 1.3 56.9 + - - +
31H TRP* 3.7 22.9 - - + -
170H LYS* 2.6 37.2 + - + +
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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