Contacts of the helix formed by residues 17 - 24 (chain B) in PDB entry 1QD6
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 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 3.3 37.4 - - - +
15B ARG 3.5 2.4 - - - -
16B GLY* 1.3 74.1 - - - +
18B ILE* 1.3 62.9 + - - +
20B ALA* 2.9 23.9 + - - +
21B ASN* 3.2 20.3 + - - +
134D ARG* 4.3 4.6 + - - -
135D ASP* 2.6 27.3 + - - -
163D MET* 3.5 6.4 - - - +
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY 3.1 9.7 + - - +
17B SER* 1.3 72.4 - - - +
19B ILE* 1.3 58.7 - - - +
21B ASN* 3.4 7.0 + - - +
22B MET* 3.0 50.6 + - + +
34D PRO 4.2 13.1 - - - +
35D TYR* 3.4 57.0 - - + +
36D ASP* 5.2 1.1 - - - -
74D ALA* 4.6 0.2 - - + -
135D ASP* 3.2 3.2 + - - -
161D ARG* 3.8 32.5 - - - +
172D GLU* 4.9 3.4 - - - +
198D LYS* 6.1 1.8 - - - +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER* 4.4 0.2 - - - +
18B ILE* 1.3 73.7 - - - +
20B ALA* 1.3 64.8 - - - +
22B MET* 3.0 27.9 + - + +
23B LEU* 3.0 26.2 + - + +
85D ASN 4.5 0.7 - - - +
87D VAL* 3.8 19.1 - - + -
119D PHE* 4.1 3.6 - - + -
121D GLY* 3.8 18.6 - - - +
122D PHE* 3.8 15.9 - - - +
123D ALA* 3.7 25.1 - - + +
135D ASP* 2.9 25.2 + - + +
136D VAL 4.8 2.0 - - - +
137D GLU* 4.0 17.3 - - + +
161D ARG* 3.9 5.4 - - - +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 4.2 8.5 + - - +
14B VAL* 3.6 17.5 - - + -
17B SER* 2.9 28.9 + - - +
19B ILE* 1.3 77.0 - - - +
21B ASN* 1.3 61.5 + - - +
23B LEU* 3.4 22.0 + - - +
24B GLN* 3.5 15.7 + - - +
123D ALA* 4.5 9.8 - - + +
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 4.8 3.5 - - + +
17B SER 3.2 12.4 + - - +
18B ILE* 3.5 10.7 + - - +
19B ILE 3.1 0.2 - - - -
20B ALA* 1.3 79.3 - - - +
22B MET* 1.3 57.3 + - - +
24B GLN* 3.0 35.6 + - - +
30C PHE* 5.1 7.2 + - - +
31C THR* 3.4 25.6 + - - -
33D TYR* 3.3 32.9 - - - +
34D PRO* 3.9 15.9 + - - +
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Residues in contact with MET 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 3.0 30.0 + - + +
19B ILE* 3.4 31.4 - - + +
21B ASN* 1.3 77.1 - - - +
23B LEU* 1.3 57.9 + - - +
24B GLN 3.2 0.2 - - - -
33D TYR* 4.0 12.8 - - + -
34D PRO 5.6 0.2 - - - +
74D ALA* 3.7 25.1 - - + -
75D PHE 4.7 1.6 - - - +
76D PRO* 3.7 31.5 - - + +
79D ARG* 2.8 30.7 + - - +
87D VAL* 4.7 12.1 - - + -
89D GLY* 5.1 0.2 - - - -
119D PHE* 3.4 39.5 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 3.0 16.6 + - + +
20B ALA* 3.6 10.3 - - - +
21B ASN 3.2 0.4 - - - -
22B MET* 1.3 73.9 - - - +
24B GLN* 1.3 62.9 + - - +
25B GLU* 3.4 7.3 + - - +
79D ARG* 3.7 23.1 + - + +
80D GLY 5.4 0.2 - - - +
84D PRO 4.3 9.0 - - - +
85D ASN* 3.9 18.6 - - + +
86D SER 3.4 27.8 - - - +
87D VAL* 4.0 15.5 - - + -
123D ALA* 3.7 30.3 - - + -
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA 3.3 26.2 + - - +
20B ALA 3.5 15.9 - - - +
21B ASN* 3.0 21.4 + - - +
23B LEU* 1.3 76.2 - - - +
25B GLU* 1.3 61.4 + - - +
30C PHE 6.3 0.9 - - - +
33D TYR* 2.7 31.9 + - + -
79D ARG* 2.8 6.6 + - - -
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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