Contacts of the strand formed by residues 22 - 28 (chain A) in PDB entry 5JPM
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 ARG 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS* 3.8 9.3 + - - +
21A PRO* 1.3 79.3 + - - +
23A LEU* 1.3 59.9 + - - +
24A LEU* 4.2 8.9 - - + +
43A LEU* 3.5 6.8 - - - +
44A GLN* 3.2 55.4 + - + +
46A VAL* 5.4 0.7 - - - +
116A TRP* 5.3 7.0 + - - +
121A LEU* 4.8 10.6 - - + +
548A TYR* 3.5 25.2 + - - -
551A ASP* 3.5 39.8 + - - -
656A ASP* 2.9 40.7 + - - +
658A ASP* 2.7 33.7 + - - +
659A GLN* 5.5 0.2 + - - -
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Residues in contact with LEU 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 ARG* 1.3 74.1 - - - +
24A LEU* 1.3 64.8 + - - +
25A LEU* 5.7 2.0 - - + -
41A VAL* 3.6 26.2 - - + -
42A GLN 3.6 15.3 - - - +
43A LEU* 3.8 17.3 - - + -
52A VAL* 5.8 1.6 - - + -
74A PHE* 4.8 11.7 - - + -
76A LEU* 4.0 8.1 - - + -
112A ALA* 4.8 18.2 - - + -
114A SER* 5.2 6.3 - - - -
116A TRP* 5.4 10.5 - - + -
117A LEU* 4.4 28.5 - - + -
121A LEU* 5.0 3.6 - - - +
128A GLN* 3.0 29.7 + - + +
656A ASP* 3.4 12.6 + - - +
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Residues in contact with LEU 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 ARG* 4.2 10.5 - - + -
23A LEU* 1.3 74.4 - - - +
25A LEU* 1.3 59.9 + - - +
26A PHE* 4.2 9.4 - - + -
40A GLY 4.0 0.2 - - - +
41A VAL* 3.5 7.8 - - - +
42A GLN* 2.5 68.3 + - + +
43A LEU* 4.9 2.9 - - - -
44A GLN* 4.9 4.0 - - + -
546A PHE* 3.7 17.7 - - + -
548A TYR* 3.3 47.3 - - + +
654A PHE* 4.1 13.7 - - + -
655A SER 3.8 2.5 - - - -
656A ASP* 3.6 16.6 - - + -
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Residues in contact with LEU 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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23A LEU* 4.0 3.1 + - + -
24A LEU* 1.3 74.3 - - - +
26A PHE* 1.3 62.4 + - - +
39A VAL* 3.7 31.0 - - + -
40A GLY 3.7 9.2 - - - +
41A VAL* 4.6 9.9 - - + -
56A VAL* 4.4 8.1 - - + -
110A LEU* 3.8 29.6 - - + +
112A ALA* 4.2 17.3 - - + +
128A GLN* 4.0 23.8 - - - +
129A GLY* 4.2 5.2 - - - -
130A ILE* 4.5 12.8 - - + +
653A ALA 3.8 0.7 - - - +
654A PHE* 3.2 3.7 - - - -
655A SER* 3.1 39.6 + - - +
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Residues in contact with PHE 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 LEU* 4.5 9.9 - - + -
25A LEU* 1.3 74.8 - - - +
27A SER* 1.3 63.1 + - - +
39A VAL* 4.2 1.6 - - - +
40A GLY* 3.0 49.2 + - - +
41A VAL* 4.9 0.4 - - - -
42A GLN* 4.4 13.7 - - + -
130A ILE* 5.7 0.2 - - - -
508A MET* 3.9 32.3 - - + -
515A ILE* 3.8 5.8 - - + +
518A MET* 3.6 31.9 - - - -
546A PHE* 3.9 26.9 - + - -
647A PHE* 4.7 5.4 - + - -
652A LEU* 4.4 14.4 - - + -
653A ALA 3.1 10.3 - - - +
654A PHE* 3.6 32.1 - + + -
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Residues in contact with SER 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 PHE* 1.3 76.2 - - - +
28A PRO* 1.3 83.0 + - - +
37A LEU* 3.7 22.2 - - - +
38A SER 4.0 3.1 + - - -
39A VAL* 4.3 1.7 - - - +
110A LEU* 3.7 25.0 - - - +
130A ILE* 4.9 5.4 - - - +
132A LEU* 3.9 5.8 - - - +
515A ILE* 4.3 2.2 - - - +
652A LEU* 3.3 6.7 - - - -
653A ALA* 2.8 32.8 + - - +
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Residues in contact with PRO 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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27A SER* 1.3 97.4 + - - +
29A SER* 1.3 66.2 + - - +
30A VAL 3.2 15.5 + - - +
37A LEU* 3.9 14.9 - - + +
38A SER* 3.1 22.4 - - - +
132A LEU* 3.4 15.1 - - - +
513A GLY 3.3 28.7 - - - +
514A GLN* 4.1 10.1 - - - +
515A ILE* 4.2 10.8 - - + +
633A LEU* 4.1 4.5 - - + -
651A GLY 3.6 8.1 - - - +
652A LEU* 3.8 5.1 - - + -
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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