Contacts of the strand formed by residues 29 - 37 (chain A) in PDB entry 1QB6
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 HIS 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A SER* 2.7 26.1 + - - +
24A LEU 3.5 5.8 + - - -
25A ASN* 4.0 5.5 - - - +
28A TYR* 1.3 83.7 - - - +
30A PHE* 1.3 61.1 + - - +
31A CYS 3.0 34.2 + - - -
32A GLY* 4.0 1.1 - - - -
61A ILE* 3.6 27.8 - - + -
127A TRP* 3.8 36.5 - + + +
137A TYR* 6.2 2.5 - + - -
181A GLY* 3.0 30.3 + - - -
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Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.1 37.0 + - + -
25A ASN 3.8 7.6 - - - -
26A SER* 3.3 25.4 - - - -
28A TYR* 3.7 20.2 - - + -
29A HIS* 1.3 81.4 - - - +
31A CYS* 1.3 85.6 + - + +
47A CYS* 3.0 30.3 - - + -
49A LYS* 3.5 22.2 - - + +
52A ILE* 3.8 22.7 - - + -
181A GLY* 4.7 9.7 + - - -
183A SER* 5.4 0.3 - - - -
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Residues in contact with CYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 2.8 35.4 + - + -
29A HIS* 3.0 17.9 + - - -
30A PHE* 1.3 99.8 - - + +
32A GLY* 1.3 62.8 + - - +
46A HIS* 5.1 1.6 - - - -
47A CYS* 2.0 53.8 - - + -
181A GLY 4.4 3.1 - - - -
183A SER* 3.1 15.0 - - - +
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Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 4.0 8.3 - - - -
22A VAL 3.3 11.2 - - - -
24A LEU* 3.8 6.2 - - - +
29A HIS* 4.0 5.3 - - - -
31A CYS* 1.3 75.6 - - - +
33A GLY* 1.3 58.0 + - - -
43A SER* 3.2 20.1 + - - -
126A GLY* 6.3 1.1 - - - -
127A TRP* 5.3 0.9 - - - -
181A GLY 4.4 3.5 + - - -
182A ASP* 4.4 2.9 + - - -
183A SER 2.7 12.8 + - - -
184A GLY* 3.3 10.8 - - - -
185A GLY* 3.9 7.2 - - - -
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Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 3.8 10.1 + - - +
22A VAL* 2.9 41.9 + - - +
24A LEU* 5.0 0.2 - - - -
32A GLY* 1.3 75.5 - - - -
34A SER* 1.3 64.5 + - - -
41A VAL* 4.2 4.7 - - - -
42A VAL 3.5 6.5 - - - -
43A SER* 4.2 1.6 - - - -
184A GLY 3.3 12.3 + - - -
185A GLY 4.0 0.4 - - - +
186A PRO* 4.0 1.8 - - - +
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Residues in contact with SER 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 3.5 6.2 + - - -
22A VAL* 5.0 0.7 - - - -
33A GLY* 1.3 74.2 + - - -
35A LEU* 1.3 62.5 + - - +
36A ILE* 3.5 2.0 + - - +
41A VAL* 3.0 8.4 - - - +
42A VAL 2.7 40.4 + - - -
109A ILE* 4.2 10.5 - - - -
184A GLY 4.7 0.7 + - - -
185A GLY 4.5 0.5 - - - -
186A PRO* 2.9 35.7 - - - +
193A LEU* 4.0 25.2 - - - +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PRO 5.6 0.2 - - - +
20A TYR* 3.2 16.7 + - - +
22A VAL* 4.5 6.2 - - + +
34A SER* 1.3 70.3 - - - +
36A ILE* 1.3 60.9 - - - +
37A ASN 3.2 22.0 - - - +
40A TRP 3.5 8.1 - - - +
41A VAL* 3.9 15.9 - - + +
56A LEU* 4.0 12.1 - - + -
96A LEU* 4.0 19.1 - - + -
100A ALA* 4.7 2.0 - - + -
102A LEU* 3.7 28.3 - - + -
106A VAL* 4.2 14.1 - - + -
107A ALA 3.6 22.2 - - - +
108A SER* 3.2 4.1 - - - -
109A ILE* 2.9 27.4 + - - +
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Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A SER 3.8 4.3 - - - +
35A LEU* 1.3 78.6 - - - +
37A ASN* 1.3 68.5 + - - +
40A TRP* 2.9 22.7 + - + +
42A VAL* 3.2 37.7 - - + -
93A LEU* 4.5 0.2 - - + -
108A SER* 3.6 11.5 + - - -
109A ILE* 3.8 27.3 - - + +
110A SER* 5.7 0.5 - - - -
111A LEU* 4.3 18.0 - - + +
193A LEU* 4.3 7.9 - - + -
222A ILE* 3.4 33.9 - - + -
226A ILE* 3.8 15.0 - - + -
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Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.2 24.5 - - - +
36A ILE* 1.3 83.8 + - - +
38A SER* 1.3 65.1 + - - +
39A GLN* 2.8 30.8 + - - +
40A TRP* 3.1 36.3 + - - +
102A LEU* 5.2 1.3 - - - -
108A SER* 3.7 10.0 - - - -
226A ILE* 4.0 15.4 - - - +
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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