Contacts of the strand formed by residues 19 - 23 (chain A) in PDB entry 1QQJ
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 TYR 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LEU 4.0 13.0 + - - -
18A PRO* 1.3 73.9 - - - +
20A GLY* 1.3 58.2 + - - +
32A ILE* 4.9 0.2 - - + -
33A GLY 3.5 3.1 - - - +
34A VAL* 3.6 25.6 - - + -
43A LEU* 4.2 13.9 - - + -
67A LEU* 3.7 24.7 - - + -
70A PHE* 3.6 30.8 - + - -
78A TRP* 4.4 4.1 + - + -
81A ALA* 3.8 16.3 - - + +
82A ARG* 4.0 11.3 + - - +
85A LEU* 3.8 19.7 - - + +
226A PHE* 3.7 21.1 - + + -
262A TRP* 3.7 2.4 - - - -
263A VAL* 2.8 47.8 + - - +
265A PRO* 4.2 17.5 - - + -
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Residues in contact with GLY 20 (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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19A TYR* 1.3 76.3 - - - +
21A VAL* 1.3 64.2 + - - +
32A ILE* 3.3 7.6 - - - +
33A GLY* 2.8 33.8 + - - +
67A LEU* 4.4 5.2 - - - -
115A MET* 4.3 3.8 - - - -
118A PRO* 4.9 0.4 - - - -
261A PRO 3.9 10.5 - - - -
262A TRP* 3.5 17.8 - - - -
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Residues in contact with VAL 21 (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 GLY* 1.3 76.1 - - - +
22A PHE* 1.3 62.5 + - - +
30A PRO* 3.6 20.9 - - + -
31A ARG 3.3 9.2 - - - +
32A ILE* 4.6 3.6 - - + -
65A THR 3.4 27.6 - - - +
66A THR* 4.1 6.7 - - - -
67A LEU* 4.4 5.8 - - + +
115A MET* 3.5 10.0 - - - +
116A HIS* 2.9 38.9 + - + +
117A LEU 3.7 15.5 - - - +
118A PRO* 3.5 29.0 - - + +
261A PRO 4.8 0.2 + - - -
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Residues in contact with PHE 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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20A GLY 4.7 0.9 - - - -
21A VAL* 1.3 76.3 - - - +
23A SER* 1.3 71.5 + - - +
24A THR* 4.3 2.0 - - + -
30A PRO* 3.4 2.4 - - - +
31A ARG* 2.9 85.1 + - + +
32A ILE 3.8 3.4 - - - -
33A GLY* 3.7 18.8 - - - -
40A ILE* 3.7 35.7 - - + -
42A ASP* 3.8 17.0 - - + -
108A THR* 4.0 18.8 - - + -
113A ALA* 4.1 5.8 - - + -
114A THR 3.2 12.1 - - - +
115A MET* 3.7 18.2 - - + -
116A HIS* 3.8 4.9 - - - -
262A TRP* 5.6 0.7 - + - -
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Residues in contact with SER 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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22A PHE* 1.3 75.7 - - - +
24A THR* 1.3 66.3 + - - +
27A ASN 3.7 5.4 - - - -
28A PRO* 3.6 25.9 + - - +
29A LYS 3.9 4.7 - - - -
31A ARG* 3.6 8.3 - - - +
113A ALA* 3.5 6.9 - - - +
114A THR* 2.8 40.2 + - - +
116A HIS* 2.8 27.3 + - - -
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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