Contacts of the strand formed by residues 21 - 30 (chain A) in PDB entry 1QPL
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 THR 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLN* 1.3 74.6 - - - +
22A CYS* 1.3 71.4 + - - +
23A VAL* 3.8 12.6 + - + +
47A LYS* 4.4 11.4 - - + -
48A PHE 3.6 17.0 - - - +
49A MET* 3.4 24.5 - - + +
106A LEU* 3.3 11.1 - - - +
107A GLU* 3.0 52.2 + - + +
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Residues in contact with CYS 22 (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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16A PRO* 4.0 32.3 - - - -
20A GLN 4.6 2.2 - - - -
21A THR* 1.3 74.6 - - - +
23A VAL* 1.3 60.9 + - - +
24A VAL* 3.8 0.9 - - + -
46A PHE 3.5 6.1 - - - +
47A LYS* 3.5 1.4 - - - -
48A PHE* 2.9 67.4 + - + -
50A LEU* 4.5 12.8 - - - -
63A VAL* 4.3 4.9 - - - -
103A LEU* 4.2 13.9 - - + -
105A LYS 4.0 4.0 - - - -
106A LEU* 4.1 4.5 - - - -
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Residues in contact with VAL 23 (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 THR* 4.3 15.9 - - + +
22A CYS* 1.3 75.0 - - - +
24A VAL* 1.3 61.1 + - - +
45A PRO* 4.1 21.8 - - + -
46A PHE 3.7 2.5 - - - -
47A LYS* 4.3 22.4 - - + +
103A LEU* 3.8 0.3 - - - -
104A LEU* 2.8 36.3 + - + +
105A LYS* 3.1 33.9 + - + +
107A GLU* 3.9 23.1 - - + +
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Residues in contact with VAL 24 (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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22A CYS* 4.4 6.7 - - + -
23A VAL* 1.3 83.2 - - - +
25A HIS* 1.3 59.2 + - - +
26A TYR* 4.5 1.3 - - + -
45A PRO* 3.3 8.5 - - - +
46A PHE* 2.7 53.6 + - + +
48A PHE* 4.3 4.7 - - + -
59A TRP* 3.5 36.1 - - + -
63A VAL* 5.0 1.3 - - + -
101A VAL* 3.7 15.7 - - + -
102A GLU 3.1 14.4 - - - +
103A LEU* 3.7 26.2 - - + -
104A LEU* 4.3 2.7 - - - +
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Residues in contact with HIS 25 (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 VAL* 1.3 75.3 - - - +
26A TYR* 1.3 63.2 + - - +
39A SER* 2.9 34.4 + - - -
40A ARG* 3.7 47.9 + - + +
43A ASN* 4.5 5.3 + - - -
44A LYS 4.0 3.8 - - - -
45A PRO* 3.7 31.3 - - + +
100A ASP 3.5 0.9 - - - +
101A VAL* 3.3 0.7 - - - +
102A GLU* 2.8 33.0 + - + +
104A LEU* 4.1 21.8 - - + -
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Residues in contact with TYR 26 (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 VAL* 4.5 0.4 - - + -
25A HIS* 1.3 77.4 - - - +
27A THR* 1.3 71.2 + - - +
37A ASP* 2.8 30.5 + - + -
38A SER* 3.4 1.0 + - - -
39A SER* 2.9 46.1 + - - -
40A ARG* 4.1 6.4 + - - +
42A ARG* 3.2 13.6 + - - -
46A PHE* 3.6 28.3 - - + -
59A TRP* 3.6 22.9 - + + -
99A PHE* 3.8 20.2 - + + -
100A ASP 2.8 15.5 - - - +
101A VAL* 4.0 7.9 - - + -
108A 587 3.4 47.2 + - + +
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Residues in contact with THR 27 (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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26A TYR* 1.3 78.7 - - - +
28A GLY* 1.3 59.7 + - - +
29A MET* 4.3 8.5 - - - +
35A LYS* 4.1 26.7 + - - +
37A ASP 3.3 9.2 - - - -
38A SER* 3.3 25.1 - - - +
40A ARG* 4.4 17.0 - - - +
41A ASP* 5.4 0.2 - - - +
71A ARG* 6.1 0.7 - - - +
98A VAL 3.9 0.2 - - - +
99A PHE* 3.4 6.9 - - - -
100A ASP* 2.9 47.5 + - + +
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Residues in contact with GLY 28 (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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26A TYR* 4.3 1.0 - - - -
27A THR* 1.3 76.2 - - - +
29A MET* 1.3 61.1 + - - -
35A LYS* 3.3 5.0 - - - +
36A PHE* 2.8 44.3 + - - -
37A ASP* 2.8 16.4 + - - +
98A VAL 3.6 5.2 - - - -
99A PHE* 3.8 13.2 - - - -
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Residues in contact with MET 29 (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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27A THR* 4.4 16.6 - - - +
28A GLY* 1.3 72.6 - - - +
30A LEU* 1.3 64.0 - - - +
33A GLY* 3.4 26.5 - - - +
34A LYS 3.3 7.2 - - - +
35A LYS* 3.8 25.1 - - + +
36A PHE* 3.4 8.1 - - - -
73A LYS* 6.4 1.1 - - - -
97A LEU* 3.8 3.5 - - - -
98A VAL* 2.9 52.4 + - + +
100A ASP* 5.5 5.4 - - - -
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Residues in contact with LEU 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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29A MET* 1.3 80.5 - - - +
31A GLU* 1.3 67.3 + - - +
32A ASP* 3.1 30.1 - - - +
33A GLY* 3.0 15.2 + - - -
34A LYS* 2.9 28.2 + - + +
36A PHE* 4.6 13.0 - - + -
90A ILE 5.6 2.5 - - - +
91A ILE* 5.0 3.1 - - + -
92A PRO* 4.8 19.7 - - + -
95A ALA* 4.3 14.1 - - + -
96A THR 4.0 7.6 - - - +
97A LEU* 3.6 27.8 - - + -
98A VAL* 4.6 5.7 - - - +
235C LYS* 5.1 10.3 - - - +
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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