Contacts of the strand formed by residues 21 - 25 (chain A) in PDB entry 1PJX
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 GLU 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLY 3.3 17.3 - - - +
20A ALA* 1.3 73.6 - - - +
22A GLY* 1.3 71.6 + - - +
23A PRO* 3.2 6.7 - - - +
33A ILE* 3.6 6.5 - - - +
34A VAL* 2.9 34.4 + - + -
36A PRO* 3.9 11.0 - - + -
74A ALA* 3.0 20.8 - - + +
120A ASN* 3.6 5.4 + - - +
229A ASP* 3.5 2.4 - - - +
271A SER* 3.4 18.1 + - - +
272A ASN* 2.8 29.7 + - - +
285A THR* 3.9 6.1 - - - +
287A HIS* 4.2 4.4 - - + +
491A CA 2.3 27.8 - - - -
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Residues in contact with GLY 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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21A GLU* 1.3 87.8 + - - +
23A PRO* 1.3 72.9 - - - +
24A VAL* 3.4 1.9 + - - +
32A TYR 3.7 5.1 - - - +
33A ILE* 4.2 1.9 - - - -
34A VAL* 4.0 3.8 - - - -
74A ALA 3.9 8.3 - - - -
75A GLY* 3.9 14.8 - - - -
76A CYS* 3.4 25.0 - - - +
272A ASN* 4.2 4.5 - - - -
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Residues in contact with PRO 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 GLU 3.2 5.5 - - - -
22A GLY* 1.3 90.6 - - - +
24A VAL* 1.3 61.1 + - - +
31A PHE* 3.8 13.9 - - + -
32A TYR 3.4 8.7 - - - +
33A ILE* 3.8 17.0 - - + -
76A CYS 4.9 2.4 - - - +
272A ASN* 3.7 19.1 - - + +
273A LEU* 3.6 32.3 - - - +
274A HIS* 3.2 25.1 + - + +
283A PHE* 4.3 5.6 - - + +
285A THR* 3.9 9.9 - - + -
492A CA 4.1 1.4 - - - -
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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 GLY 3.8 2.9 - - - +
23A PRO* 1.3 74.8 - - - +
25A PHE* 1.3 75.9 + - - +
31A PHE* 3.4 7.6 - - - -
32A TYR* 2.9 51.5 + - + -
76A CYS* 3.6 27.1 - - + +
77A GLN* 4.1 9.2 - - - -
78A CYS* 3.8 25.8 - - + +
85A LEU* 4.1 13.0 - - + -
274A HIS* 3.7 17.0 - - + +
304A GLN* 5.6 0.2 - - - +
306A CYS* 6.3 0.2 - - - -
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Residues in contact with PHE 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 79.5 - - - +
26A ASP* 1.3 65.5 + - - +
29A GLY* 3.5 26.2 - - - -
30A ASP 3.2 8.3 - - - -
31A PHE* 3.5 36.8 - + + -
32A TYR* 5.0 0.7 - - - -
53A LEU* 3.9 10.8 - - + -
78A CYS* 3.5 17.0 - - - +
274A HIS* 3.8 12.6 + + + +
275A PHE 3.5 19.1 - - - -
276A LYS* 3.5 33.9 - - + -
277A PRO* 3.8 22.7 - - + -
283A PHE* 3.7 26.0 - + - -
306A CYS* 4.2 8.0 - - - -
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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